Commit 068afdb6 authored by ziegenhain@bio.lmu.de's avatar ziegenhain@bio.lmu.de
Browse files

Add Example run data for the new zUMIs version

parent 1fb3a288

ExampleData/ExampleRun_config.yaml

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###########################################

#Welcome to zUMIs

#below, please fill the mandatory inputs

#We expect full paths for all files.

###########################################



#define a project name

project: tiny



#Sequencing File Inputs:

#For each input file, make one list object & define path and barcode ranges

#base definition vocabulary: BC(n) UMI(n) cDNA(n).

#Barcode range definition needs to account for all ranges. You can give several comma-separated ranges for BC & UMI sequences, eg. BC(1-6,20-26)

sequence_files:

  file1:

    name: /data/share/common/scripts/UMI_pipeline/zUMIs/ExampleData/barcoderead_HEK.1mio.fq.gz

    base_definition:

      - BC(1-6)

      - UMI(7-16)

  file2:

    name: /data/share/common/scripts/UMI_pipeline/zUMIs/ExampleData/cDNAread_HEK.1mio.fq.gz

    base_definition:

      - cDNA(1-50)



#STAR reference genome setup

reference:

  STAR_index: /data/ngs/genomes/Human/hg38/STAR5idx_noGTF

  GTF_file: /data/ngs/genomes/Human/hg38/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf

  additional_files:

    - /data/ngs/genomes/artificial_sequences/spikes/ERCC92.fa #possible additional reference sequences, eg ERCC.fa

  additional_STAR_params: null #add custom mapping parameters to STAR



#output directory

out_dir: /data/share/htp/zUMIs2/onemillion



###########################################

#below, you may optionally change default parameters

###########################################



#number of processors to use

num_threads: 12

mem_limit: 50 #Memory limit in Gigabytes, null meaning unlimited RAM usage.



#barcode & UMI filtering options

#number of bases under the base quality cutoff that should be filtered out.

#Phred score base-cutoff for quality control.

filter_cutoffs:

  BC_filter:

    num_bases: 1

    phred: 20

  UMI_filter:

    num_bases: 1

    phred: 20



#Options for Barcode handling

#You can give either number of top barcodes to use or give an annotation of cell barcodes.

#If you leave both barcode_num and barcode_file empty, zUMIs will perform automatic cell barcode selection for you!

barcodes:

  barcode_num: null

  barcode_file: null

  BarcodeBinning: 0 #Hamming distance binning of close cell barcode sequences. ATTENTION! This option is currently not implemented!

  nReadsperCell: 100 #Keep only the cell barcodes with atleast n number of reads.



#Options related to counting of reads towards expression profiles

counting_opts:

  introns: yes #can be set to no for exon-only counting.

  downsampling: 0 #Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000) Barcodes with less than <d> will not be reported. 0 means adaptive downsampling. Default: 0.

  strand: 0 #Is the library stranded? 0 = unstranded, 1 = positively stranded, 2 = negatively stranded

  Ham_Dist: 0 #Hamming distance collapsing of UMI sequences.

  velocyto: no #Would you like velocyto-compatible counting of intron-exon spanning reads

  primaryHit: yes #Do you want to count the primary Hits of multimapping reads towards gene expression levels?



#produce stats files and plots?

make_stats: yes



#use SLURM workload manger?

use_SLURM: no



#Start zUMIs from stage. Possible TEXT(Filtering, Mapping, Counting, Summarising). Default: Filtering.

which_Stage: Filtering



#below, the fqfilter will add a read_layout flag defining SE or PE

samtools_exec: samtools

pigz_exec: pigz

STAR_exec: STAR

zUMIs_directory: /data/share/htp/zUMIs2/zUMIs

read_layout: SE

ExampleData/additional_sequence_annot.gtf

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+92 −0
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ERCC-00002	User	exon	1	1061	.	+	.	gene_id "ERCC-00002"; transcript_id "ERCC-00002"; exon_number "1"; gene_name "ERCC-00002"; gene_biotype "User"; transcript_name "ERCC-00002"; exon_id "ERCC-00002"

ERCC-00003	User	exon	1	1023	.	+	.	gene_id "ERCC-00003"; transcript_id "ERCC-00003"; exon_number "1"; gene_name "ERCC-00003"; gene_biotype "User"; transcript_name "ERCC-00003"; exon_id "ERCC-00003"

ERCC-00004	User	exon	1	523	.	+	.	gene_id "ERCC-00004"; transcript_id "ERCC-00004"; exon_number "1"; gene_name "ERCC-00004"; gene_biotype "User"; transcript_name "ERCC-00004"; exon_id "ERCC-00004"

ERCC-00009	User	exon	1	984	.	+	.	gene_id "ERCC-00009"; transcript_id "ERCC-00009"; exon_number "1"; gene_name "ERCC-00009"; gene_biotype "User"; transcript_name "ERCC-00009"; exon_id "ERCC-00009"

ERCC-00012	User	exon	1	994	.	+	.	gene_id "ERCC-00012"; transcript_id "ERCC-00012"; exon_number "1"; gene_name "ERCC-00012"; gene_biotype "User"; transcript_name "ERCC-00012"; exon_id "ERCC-00012"

ERCC-00013	User	exon	1	808	.	+	.	gene_id "ERCC-00013"; transcript_id "ERCC-00013"; exon_number "1"; gene_name "ERCC-00013"; gene_biotype "User"; transcript_name "ERCC-00013"; exon_id "ERCC-00013"

ERCC-00014	User	exon	1	1957	.	+	.	gene_id "ERCC-00014"; transcript_id "ERCC-00014"; exon_number "1"; gene_name "ERCC-00014"; gene_biotype "User"; transcript_name "ERCC-00014"; exon_id "ERCC-00014"

ERCC-00016	User	exon	1	844	.	+	.	gene_id "ERCC-00016"; transcript_id "ERCC-00016"; exon_number "1"; gene_name "ERCC-00016"; gene_biotype "User"; transcript_name "ERCC-00016"; exon_id "ERCC-00016"

ERCC-00017	User	exon	1	1136	.	+	.	gene_id "ERCC-00017"; transcript_id "ERCC-00017"; exon_number "1"; gene_name "ERCC-00017"; gene_biotype "User"; transcript_name "ERCC-00017"; exon_id "ERCC-00017"

ERCC-00019	User	exon	1	644	.	+	.	gene_id "ERCC-00019"; transcript_id "ERCC-00019"; exon_number "1"; gene_name "ERCC-00019"; gene_biotype "User"; transcript_name "ERCC-00019"; exon_id "ERCC-00019"

ERCC-00022	User	exon	1	751	.	+	.	gene_id "ERCC-00022"; transcript_id "ERCC-00022"; exon_number "1"; gene_name "ERCC-00022"; gene_biotype "User"; transcript_name "ERCC-00022"; exon_id "ERCC-00022"

ERCC-00024	User	exon	1	536	.	+	.	gene_id "ERCC-00024"; transcript_id "ERCC-00024"; exon_number "1"; gene_name "ERCC-00024"; gene_biotype "User"; transcript_name "ERCC-00024"; exon_id "ERCC-00024"

ERCC-00025	User	exon	1	1994	.	+	.	gene_id "ERCC-00025"; transcript_id "ERCC-00025"; exon_number "1"; gene_name "ERCC-00025"; gene_biotype "User"; transcript_name "ERCC-00025"; exon_id "ERCC-00025"

ERCC-00028	User	exon	1	1130	.	+	.	gene_id "ERCC-00028"; transcript_id "ERCC-00028"; exon_number "1"; gene_name "ERCC-00028"; gene_biotype "User"; transcript_name "ERCC-00028"; exon_id "ERCC-00028"

ERCC-00031	User	exon	1	1138	.	+	.	gene_id "ERCC-00031"; transcript_id "ERCC-00031"; exon_number "1"; gene_name "ERCC-00031"; gene_biotype "User"; transcript_name "ERCC-00031"; exon_id "ERCC-00031"

ERCC-00033	User	exon	1	2022	.	+	.	gene_id "ERCC-00033"; transcript_id "ERCC-00033"; exon_number "1"; gene_name "ERCC-00033"; gene_biotype "User"; transcript_name "ERCC-00033"; exon_id "ERCC-00033"

ERCC-00034	User	exon	1	1019	.	+	.	gene_id "ERCC-00034"; transcript_id "ERCC-00034"; exon_number "1"; gene_name "ERCC-00034"; gene_biotype "User"; transcript_name "ERCC-00034"; exon_id "ERCC-00034"

ERCC-00035	User	exon	1	1130	.	+	.	gene_id "ERCC-00035"; transcript_id "ERCC-00035"; exon_number "1"; gene_name "ERCC-00035"; gene_biotype "User"; transcript_name "ERCC-00035"; exon_id "ERCC-00035"

ERCC-00039	User	exon	1	740	.	+	.	gene_id "ERCC-00039"; transcript_id "ERCC-00039"; exon_number "1"; gene_name "ERCC-00039"; gene_biotype "User"; transcript_name "ERCC-00039"; exon_id "ERCC-00039"

ERCC-00040	User	exon	1	744	.	+	.	gene_id "ERCC-00040"; transcript_id "ERCC-00040"; exon_number "1"; gene_name "ERCC-00040"; gene_biotype "User"; transcript_name "ERCC-00040"; exon_id "ERCC-00040"

ERCC-00041	User	exon	1	1122	.	+	.	gene_id "ERCC-00041"; transcript_id "ERCC-00041"; exon_number "1"; gene_name "ERCC-00041"; gene_biotype "User"; transcript_name "ERCC-00041"; exon_id "ERCC-00041"

ERCC-00042	User	exon	1	1023	.	+	.	gene_id "ERCC-00042"; transcript_id "ERCC-00042"; exon_number "1"; gene_name "ERCC-00042"; gene_biotype "User"; transcript_name "ERCC-00042"; exon_id "ERCC-00042"

ERCC-00043	User	exon	1	1023	.	+	.	gene_id "ERCC-00043"; transcript_id "ERCC-00043"; exon_number "1"; gene_name "ERCC-00043"; gene_biotype "User"; transcript_name "ERCC-00043"; exon_id "ERCC-00043"

ERCC-00044	User	exon	1	1156	.	+	.	gene_id "ERCC-00044"; transcript_id "ERCC-00044"; exon_number "1"; gene_name "ERCC-00044"; gene_biotype "User"; transcript_name "ERCC-00044"; exon_id "ERCC-00044"

ERCC-00046	User	exon	1	522	.	+	.	gene_id "ERCC-00046"; transcript_id "ERCC-00046"; exon_number "1"; gene_name "ERCC-00046"; gene_biotype "User"; transcript_name "ERCC-00046"; exon_id "ERCC-00046"

ERCC-00048	User	exon	1	992	.	+	.	gene_id "ERCC-00048"; transcript_id "ERCC-00048"; exon_number "1"; gene_name "ERCC-00048"; gene_biotype "User"; transcript_name "ERCC-00048"; exon_id "ERCC-00048"

ERCC-00051	User	exon	1	274	.	+	.	gene_id "ERCC-00051"; transcript_id "ERCC-00051"; exon_number "1"; gene_name "ERCC-00051"; gene_biotype "User"; transcript_name "ERCC-00051"; exon_id "ERCC-00051"

ERCC-00053	User	exon	1	1023	.	+	.	gene_id "ERCC-00053"; transcript_id "ERCC-00053"; exon_number "1"; gene_name "ERCC-00053"; gene_biotype "User"; transcript_name "ERCC-00053"; exon_id "ERCC-00053"

ERCC-00054	User	exon	1	274	.	+	.	gene_id "ERCC-00054"; transcript_id "ERCC-00054"; exon_number "1"; gene_name "ERCC-00054"; gene_biotype "User"; transcript_name "ERCC-00054"; exon_id "ERCC-00054"

ERCC-00057	User	exon	1	1021	.	+	.	gene_id "ERCC-00057"; transcript_id "ERCC-00057"; exon_number "1"; gene_name "ERCC-00057"; gene_biotype "User"; transcript_name "ERCC-00057"; exon_id "ERCC-00057"

ERCC-00058	User	exon	1	1136	.	+	.	gene_id "ERCC-00058"; transcript_id "ERCC-00058"; exon_number "1"; gene_name "ERCC-00058"; gene_biotype "User"; transcript_name "ERCC-00058"; exon_id "ERCC-00058"

ERCC-00059	User	exon	1	525	.	+	.	gene_id "ERCC-00059"; transcript_id "ERCC-00059"; exon_number "1"; gene_name "ERCC-00059"; gene_biotype "User"; transcript_name "ERCC-00059"; exon_id "ERCC-00059"

ERCC-00060	User	exon	1	523	.	+	.	gene_id "ERCC-00060"; transcript_id "ERCC-00060"; exon_number "1"; gene_name "ERCC-00060"; gene_biotype "User"; transcript_name "ERCC-00060"; exon_id "ERCC-00060"

ERCC-00061	User	exon	1	1136	.	+	.	gene_id "ERCC-00061"; transcript_id "ERCC-00061"; exon_number "1"; gene_name "ERCC-00061"; gene_biotype "User"; transcript_name "ERCC-00061"; exon_id "ERCC-00061"

ERCC-00062	User	exon	1	1023	.	+	.	gene_id "ERCC-00062"; transcript_id "ERCC-00062"; exon_number "1"; gene_name "ERCC-00062"; gene_biotype "User"; transcript_name "ERCC-00062"; exon_id "ERCC-00062"

ERCC-00067	User	exon	1	644	.	+	.	gene_id "ERCC-00067"; transcript_id "ERCC-00067"; exon_number "1"; gene_name "ERCC-00067"; gene_biotype "User"; transcript_name "ERCC-00067"; exon_id "ERCC-00067"

ERCC-00069	User	exon	1	1137	.	+	.	gene_id "ERCC-00069"; transcript_id "ERCC-00069"; exon_number "1"; gene_name "ERCC-00069"; gene_biotype "User"; transcript_name "ERCC-00069"; exon_id "ERCC-00069"

ERCC-00071	User	exon	1	642	.	+	.	gene_id "ERCC-00071"; transcript_id "ERCC-00071"; exon_number "1"; gene_name "ERCC-00071"; gene_biotype "User"; transcript_name "ERCC-00071"; exon_id "ERCC-00071"

ERCC-00073	User	exon	1	603	.	+	.	gene_id "ERCC-00073"; transcript_id "ERCC-00073"; exon_number "1"; gene_name "ERCC-00073"; gene_biotype "User"; transcript_name "ERCC-00073"; exon_id "ERCC-00073"

ERCC-00074	User	exon	1	522	.	+	.	gene_id "ERCC-00074"; transcript_id "ERCC-00074"; exon_number "1"; gene_name "ERCC-00074"; gene_biotype "User"; transcript_name "ERCC-00074"; exon_id "ERCC-00074"

ERCC-00075	User	exon	1	1023	.	+	.	gene_id "ERCC-00075"; transcript_id "ERCC-00075"; exon_number "1"; gene_name "ERCC-00075"; gene_biotype "User"; transcript_name "ERCC-00075"; exon_id "ERCC-00075"

ERCC-00076	User	exon	1	642	.	+	.	gene_id "ERCC-00076"; transcript_id "ERCC-00076"; exon_number "1"; gene_name "ERCC-00076"; gene_biotype "User"; transcript_name "ERCC-00076"; exon_id "ERCC-00076"

ERCC-00077	User	exon	1	273	.	+	.	gene_id "ERCC-00077"; transcript_id "ERCC-00077"; exon_number "1"; gene_name "ERCC-00077"; gene_biotype "User"; transcript_name "ERCC-00077"; exon_id "ERCC-00077"

ERCC-00078	User	exon	1	993	.	+	.	gene_id "ERCC-00078"; transcript_id "ERCC-00078"; exon_number "1"; gene_name "ERCC-00078"; gene_biotype "User"; transcript_name "ERCC-00078"; exon_id "ERCC-00078"

ERCC-00079	User	exon	1	644	.	+	.	gene_id "ERCC-00079"; transcript_id "ERCC-00079"; exon_number "1"; gene_name "ERCC-00079"; gene_biotype "User"; transcript_name "ERCC-00079"; exon_id "ERCC-00079"

ERCC-00081	User	exon	1	534	.	+	.	gene_id "ERCC-00081"; transcript_id "ERCC-00081"; exon_number "1"; gene_name "ERCC-00081"; gene_biotype "User"; transcript_name "ERCC-00081"; exon_id "ERCC-00081"

ERCC-00083	User	exon	1	1022	.	+	.	gene_id "ERCC-00083"; transcript_id "ERCC-00083"; exon_number "1"; gene_name "ERCC-00083"; gene_biotype "User"; transcript_name "ERCC-00083"; exon_id "ERCC-00083"

ERCC-00084	User	exon	1	994	.	+	.	gene_id "ERCC-00084"; transcript_id "ERCC-00084"; exon_number "1"; gene_name "ERCC-00084"; gene_biotype "User"; transcript_name "ERCC-00084"; exon_id "ERCC-00084"

ERCC-00085	User	exon	1	844	.	+	.	gene_id "ERCC-00085"; transcript_id "ERCC-00085"; exon_number "1"; gene_name "ERCC-00085"; gene_biotype "User"; transcript_name "ERCC-00085"; exon_id "ERCC-00085"

ERCC-00086	User	exon	1	1020	.	+	.	gene_id "ERCC-00086"; transcript_id "ERCC-00086"; exon_number "1"; gene_name "ERCC-00086"; gene_biotype "User"; transcript_name "ERCC-00086"; exon_id "ERCC-00086"

ERCC-00092	User	exon	1	1124	.	+	.	gene_id "ERCC-00092"; transcript_id "ERCC-00092"; exon_number "1"; gene_name "ERCC-00092"; gene_biotype "User"; transcript_name "ERCC-00092"; exon_id "ERCC-00092"

ERCC-00095	User	exon	1	521	.	+	.	gene_id "ERCC-00095"; transcript_id "ERCC-00095"; exon_number "1"; gene_name "ERCC-00095"; gene_biotype "User"; transcript_name "ERCC-00095"; exon_id "ERCC-00095"

ERCC-00096	User	exon	1	1107	.	+	.	gene_id "ERCC-00096"; transcript_id "ERCC-00096"; exon_number "1"; gene_name "ERCC-00096"; gene_biotype "User"; transcript_name "ERCC-00096"; exon_id "ERCC-00096"

ERCC-00097	User	exon	1	523	.	+	.	gene_id "ERCC-00097"; transcript_id "ERCC-00097"; exon_number "1"; gene_name "ERCC-00097"; gene_biotype "User"; transcript_name "ERCC-00097"; exon_id "ERCC-00097"

ERCC-00098	User	exon	1	1143	.	+	.	gene_id "ERCC-00098"; transcript_id "ERCC-00098"; exon_number "1"; gene_name "ERCC-00098"; gene_biotype "User"; transcript_name "ERCC-00098"; exon_id "ERCC-00098"

ERCC-00099	User	exon	1	1350	.	+	.	gene_id "ERCC-00099"; transcript_id "ERCC-00099"; exon_number "1"; gene_name "ERCC-00099"; gene_biotype "User"; transcript_name "ERCC-00099"; exon_id "ERCC-00099"

ERCC-00104	User	exon	1	2022	.	+	.	gene_id "ERCC-00104"; transcript_id "ERCC-00104"; exon_number "1"; gene_name "ERCC-00104"; gene_biotype "User"; transcript_name "ERCC-00104"; exon_id "ERCC-00104"

ERCC-00108	User	exon	1	1022	.	+	.	gene_id "ERCC-00108"; transcript_id "ERCC-00108"; exon_number "1"; gene_name "ERCC-00108"; gene_biotype "User"; transcript_name "ERCC-00108"; exon_id "ERCC-00108"

ERCC-00109	User	exon	1	536	.	+	.	gene_id "ERCC-00109"; transcript_id "ERCC-00109"; exon_number "1"; gene_name "ERCC-00109"; gene_biotype "User"; transcript_name "ERCC-00109"; exon_id "ERCC-00109"

ERCC-00111	User	exon	1	994	.	+	.	gene_id "ERCC-00111"; transcript_id "ERCC-00111"; exon_number "1"; gene_name "ERCC-00111"; gene_biotype "User"; transcript_name "ERCC-00111"; exon_id "ERCC-00111"

ERCC-00112	User	exon	1	1136	.	+	.	gene_id "ERCC-00112"; transcript_id "ERCC-00112"; exon_number "1"; gene_name "ERCC-00112"; gene_biotype "User"; transcript_name "ERCC-00112"; exon_id "ERCC-00112"

ERCC-00113	User	exon	1	840	.	+	.	gene_id "ERCC-00113"; transcript_id "ERCC-00113"; exon_number "1"; gene_name "ERCC-00113"; gene_biotype "User"; transcript_name "ERCC-00113"; exon_id "ERCC-00113"

ERCC-00116	User	exon	1	1991	.	+	.	gene_id "ERCC-00116"; transcript_id "ERCC-00116"; exon_number "1"; gene_name "ERCC-00116"; gene_biotype "User"; transcript_name "ERCC-00116"; exon_id "ERCC-00116"

ERCC-00117	User	exon	1	1136	.	+	.	gene_id "ERCC-00117"; transcript_id "ERCC-00117"; exon_number "1"; gene_name "ERCC-00117"; gene_biotype "User"; transcript_name "ERCC-00117"; exon_id "ERCC-00117"

ERCC-00120	User	exon	1	536	.	+	.	gene_id "ERCC-00120"; transcript_id "ERCC-00120"; exon_number "1"; gene_name "ERCC-00120"; gene_biotype "User"; transcript_name "ERCC-00120"; exon_id "ERCC-00120"

ERCC-00123	User	exon	1	1022	.	+	.	gene_id "ERCC-00123"; transcript_id "ERCC-00123"; exon_number "1"; gene_name "ERCC-00123"; gene_biotype "User"; transcript_name "ERCC-00123"; exon_id "ERCC-00123"

ERCC-00126	User	exon	1	1118	.	+	.	gene_id "ERCC-00126"; transcript_id "ERCC-00126"; exon_number "1"; gene_name "ERCC-00126"; gene_biotype "User"; transcript_name "ERCC-00126"; exon_id "ERCC-00126"

ERCC-00130	User	exon	1	1059	.	+	.	gene_id "ERCC-00130"; transcript_id "ERCC-00130"; exon_number "1"; gene_name "ERCC-00130"; gene_biotype "User"; transcript_name "ERCC-00130"; exon_id "ERCC-00130"

ERCC-00131	User	exon	1	771	.	+	.	gene_id "ERCC-00131"; transcript_id "ERCC-00131"; exon_number "1"; gene_name "ERCC-00131"; gene_biotype "User"; transcript_name "ERCC-00131"; exon_id "ERCC-00131"

ERCC-00134	User	exon	1	274	.	+	.	gene_id "ERCC-00134"; transcript_id "ERCC-00134"; exon_number "1"; gene_name "ERCC-00134"; gene_biotype "User"; transcript_name "ERCC-00134"; exon_id "ERCC-00134"

ERCC-00136	User	exon	1	1033	.	+	.	gene_id "ERCC-00136"; transcript_id "ERCC-00136"; exon_number "1"; gene_name "ERCC-00136"; gene_biotype "User"; transcript_name "ERCC-00136"; exon_id "ERCC-00136"

ERCC-00137	User	exon	1	537	.	+	.	gene_id "ERCC-00137"; transcript_id "ERCC-00137"; exon_number "1"; gene_name "ERCC-00137"; gene_biotype "User"; transcript_name "ERCC-00137"; exon_id "ERCC-00137"

ERCC-00138	User	exon	1	1024	.	+	.	gene_id "ERCC-00138"; transcript_id "ERCC-00138"; exon_number "1"; gene_name "ERCC-00138"; gene_biotype "User"; transcript_name "ERCC-00138"; exon_id "ERCC-00138"

ERCC-00142	User	exon	1	493	.	+	.	gene_id "ERCC-00142"; transcript_id "ERCC-00142"; exon_number "1"; gene_name "ERCC-00142"; gene_biotype "User"; transcript_name "ERCC-00142"; exon_id "ERCC-00142"

ERCC-00143	User	exon	1	784	.	+	.	gene_id "ERCC-00143"; transcript_id "ERCC-00143"; exon_number "1"; gene_name "ERCC-00143"; gene_biotype "User"; transcript_name "ERCC-00143"; exon_id "ERCC-00143"

ERCC-00144	User	exon	1	538	.	+	.	gene_id "ERCC-00144"; transcript_id "ERCC-00144"; exon_number "1"; gene_name "ERCC-00144"; gene_biotype "User"; transcript_name "ERCC-00144"; exon_id "ERCC-00144"

ERCC-00145	User	exon	1	1042	.	+	.	gene_id "ERCC-00145"; transcript_id "ERCC-00145"; exon_number "1"; gene_name "ERCC-00145"; gene_biotype "User"; transcript_name "ERCC-00145"; exon_id "ERCC-00145"

ERCC-00147	User	exon	1	1023	.	+	.	gene_id "ERCC-00147"; transcript_id "ERCC-00147"; exon_number "1"; gene_name "ERCC-00147"; gene_biotype "User"; transcript_name "ERCC-00147"; exon_id "ERCC-00147"

ERCC-00148	User	exon	1	494	.	+	.	gene_id "ERCC-00148"; transcript_id "ERCC-00148"; exon_number "1"; gene_name "ERCC-00148"; gene_biotype "User"; transcript_name "ERCC-00148"; exon_id "ERCC-00148"

ERCC-00150	User	exon	1	743	.	+	.	gene_id "ERCC-00150"; transcript_id "ERCC-00150"; exon_number "1"; gene_name "ERCC-00150"; gene_biotype "User"; transcript_name "ERCC-00150"; exon_id "ERCC-00150"

ERCC-00154	User	exon	1	537	.	+	.	gene_id "ERCC-00154"; transcript_id "ERCC-00154"; exon_number "1"; gene_name "ERCC-00154"; gene_biotype "User"; transcript_name "ERCC-00154"; exon_id "ERCC-00154"

ERCC-00156	User	exon	1	494	.	+	.	gene_id "ERCC-00156"; transcript_id "ERCC-00156"; exon_number "1"; gene_name "ERCC-00156"; gene_biotype "User"; transcript_name "ERCC-00156"; exon_id "ERCC-00156"

ERCC-00157	User	exon	1	1019	.	+	.	gene_id "ERCC-00157"; transcript_id "ERCC-00157"; exon_number "1"; gene_name "ERCC-00157"; gene_biotype "User"; transcript_name "ERCC-00157"; exon_id "ERCC-00157"

ERCC-00158	User	exon	1	1027	.	+	.	gene_id "ERCC-00158"; transcript_id "ERCC-00158"; exon_number "1"; gene_name "ERCC-00158"; gene_biotype "User"; transcript_name "ERCC-00158"; exon_id "ERCC-00158"

ERCC-00160	User	exon	1	743	.	+	.	gene_id "ERCC-00160"; transcript_id "ERCC-00160"; exon_number "1"; gene_name "ERCC-00160"; gene_biotype "User"; transcript_name "ERCC-00160"; exon_id "ERCC-00160"

ERCC-00162	User	exon	1	523	.	+	.	gene_id "ERCC-00162"; transcript_id "ERCC-00162"; exon_number "1"; gene_name "ERCC-00162"; gene_biotype "User"; transcript_name "ERCC-00162"; exon_id "ERCC-00162"

ERCC-00163	User	exon	1	543	.	+	.	gene_id "ERCC-00163"; transcript_id "ERCC-00163"; exon_number "1"; gene_name "ERCC-00163"; gene_biotype "User"; transcript_name "ERCC-00163"; exon_id "ERCC-00163"

ERCC-00164	User	exon	1	1022	.	+	.	gene_id "ERCC-00164"; transcript_id "ERCC-00164"; exon_number "1"; gene_name "ERCC-00164"; gene_biotype "User"; transcript_name "ERCC-00164"; exon_id "ERCC-00164"

ERCC-00165	User	exon	1	872	.	+	.	gene_id "ERCC-00165"; transcript_id "ERCC-00165"; exon_number "1"; gene_name "ERCC-00165"; gene_biotype "User"; transcript_name "ERCC-00165"; exon_id "ERCC-00165"

ERCC-00168	User	exon	1	1024	.	+	.	gene_id "ERCC-00168"; transcript_id "ERCC-00168"; exon_number "1"; gene_name "ERCC-00168"; gene_biotype "User"; transcript_name "ERCC-00168"; exon_id "ERCC-00168"

ERCC-00170	User	exon	1	1023	.	+	.	gene_id "ERCC-00170"; transcript_id "ERCC-00170"; exon_number "1"; gene_name "ERCC-00170"; gene_biotype "User"; transcript_name "ERCC-00170"; exon_id "ERCC-00170"

ERCC-00171	User	exon	1	505	.	+	.	gene_id "ERCC-00171"; transcript_id "ERCC-00171"; exon_number "1"; gene_name "ERCC-00171"; gene_biotype "User"; transcript_name "ERCC-00171"; exon_id "ERCC-00171"

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Original line number Diff line number Diff line 
                                 Started job on |	Jun 05 14:42:14

                             Started mapping on |	Jun 05 15:02:45

                                    Finished on |	Jun 05 15:03:09

       Mapping speed, Million of reads per hour |	127.99



                          Number of input reads |	853296

                      Average input read length |	50

                                    UNIQUE READS:

                   Uniquely mapped reads number |	531649

                        Uniquely mapped reads % |	62.31%

                          Average mapped length |	49.33

                       Number of splices: Total |	36123

            Number of splices: Annotated (sjdb) |	35554

                       Number of splices: GT/AG |	35561

                       Number of splices: GC/AG |	199

                       Number of splices: AT/AC |	41

               Number of splices: Non-canonical |	322

                      Mismatch rate per base, % |	0.31%

                         Deletion rate per base |	0.01%

                        Deletion average length |	1.22

                        Insertion rate per base |	0.01%

                       Insertion average length |	1.25

                             MULTI-MAPPING READS:

        Number of reads mapped to multiple loci |	278254

             % of reads mapped to multiple loci |	32.61%

        Number of reads mapped to too many loci |	23

             % of reads mapped to too many loci |	0.00%

                                  UNMAPPED READS:

       % of reads unmapped: too many mismatches |	0.00%

                 % of reads unmapped: too short |	4.40%

                     % of reads unmapped: other |	0.68%

                                  CHIMERIC READS:

                       Number of chimeric reads |	0

                            % of chimeric reads |	0.00%

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