Commit cb4ee6d3 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct ICELL8 case for consistency

parent 5a9a5be8

README.md

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@@ -31,7 +31,7 @@ Details on the [Docker image](#Docker) are given below. 


In principle, any technology with a cell barcode and unique molecular identifier (UMI) can be supported.



The following technologies have been tested to ensure that they give the expected results: 10x Genomics, Nadia (DropSeq), iCELL8 version 3 

The following technologies have been tested to ensure that they give the expected results: 10x Genomics, Nadia (DropSeq), ICELL8 version 3 



We provide the following preset configurations for convenience based on published data and configurations used by other pipelines 

(e.g, DropSeqPipe and Kallisto/Bustools). To add further support for other technologies or troubleshoot problems, please submit an Issue
@@ -52,7 +52,7 @@ avoid causing problems with existing runs). Multiple samples of the same technol 
-  CEL-Seq (8bp barcode, 4bp UMI): celseq

-  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

-  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

-  ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

- inDrops

    -  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2
@@ -631,7 +631,7 @@ The script will: 


### Valid barcodes



Please note that this script alters the barcode whitelist. Known iCELL8 barcodes are supported but this is not possible with Nadia or DropSeq chemistry so 100% valid barcodes will be returned.

Please note that this script alters the barcode whitelist. Known ICELL8 barcodes are supported but this is not possible with Nadia or DropSeq chemistry so 100% valid barcodes will be returned.



### Manual <span id="Help"><span>
@@ -718,7 +718,7 @@ Usage: 
  bash launch_universc.sh -v

  bash launch_universc.sh -h



Convert sequencing data (FASTQ) from Nadia or iCELL8 platforms for compatibility with 10x Genomics and run cellranger count

Convert sequencing data (FASTQ) from Nadia or ICELL8 platforms for compatibility with 10x Genomics and run cellranger count



Mandatory arguments to long options are mandatory for short options too.

       --testrun                Initiates a test trun with the test dataset
@@ -738,7 +738,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

                                  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
@@ -850,7 +850,7 @@ bash universc/launch_universc.sh --id "test-dropseq" --technology "nadia" \ 
 --read2 "universc/test/shared/dropseq-test/SRR1873277_S1_L001_R2_001" 

```



#### Running launch_universc.sh on iCELL8 data

#### Running launch_universc.sh on ICELL8 data



- add example running on custom barcode whitelist

launch_universc.sh

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@@ -130,7 +130,7 @@ Usage: 
  '$SHELL' '$invocation' -v

  '$SHELL' '$invocation' -h



Convert sequencing data (FASTQ) from Nadia or iCELL8 platforms for compatibility with 10x Genomics and run cellranger count

Convert sequencing data (FASTQ) from Nadia or ICELL8 platforms for compatibility with 10x Genomics and run cellranger count



Mandatory arguments to long options are mandatory for short options too.

       --testrun                Initiates a test trun with the test dataset
@@ -150,7 +150,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

                                  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
@@ -943,8 +943,8 @@ else 
    if [[ "$technology" == "10x"* ]]; then

        barcodefile="default:10x"

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${whitelistdir}/iCell8_barcode.txt

	echo "***WARNING: selected barcode file (${barcodefile}) contains barcodes for all wells in iCell8. valid barcode will be an overestimate***"

        barcodefile=${whitelistdir}/ICELL8_barcode.txt

	echo "***WARNING: selected barcode file (${barcodefile}) contains barcodes for all wells in ICELL8. valid barcode will be an overestimate***"

    elif [[ "$technology" == "quartz-seq2-384" ]]; then

        barcodefile=${whitelistdir}/Quartz-Seq2-384_barcode.txt

    elif [[ "$technology" == "quartz-seq2-1536" ]]; then

man/convert.sh

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@@ -100,7 +100,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

                                  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
@@ -117,7 +117,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 


           A barcode whitelist is provided for all beads or wells for the following technologies:



                 10x Genomics, iCell8, inDrops-v2, and QuartzSeq2

                 10x Genomics, ICELL8, inDrops-v2, and QuartzSeq2



            Where no known barcodes are available all possible barcodes of the expected length are

            generated and converted if the permutations have not been computed already.

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