Use smaller test data

git clone https://github.com/haowenz/chromap.git

cd chromap && make

# create an index first and then map

./chromap -i -r test/ref.fa.gz -o ref.index

./chromap -x ref.index -r test/ref.fa.gz -1 test/read1.fq.gz -o test.bed

./chromap -i -r test/ref.fa -o ref.index

./chromap -x ref.index -r test/ref.fa -1 test/read1.fq -2 test/read2.fq -o test.bed

# use presets (no test data)

./chromap --preset atac -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o aln.bed       # ATAC-seq reads

./chromap --preset atac -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o aln.bed \

./chromap --preset atac -x index -r ref.fa -1 read1.fq -2 read2.fq -o aln.bed       # ATAC-seq reads

./chromap --preset atac -x index -r ref.fa -1 read1.fq -2 read2.fq -o aln.bed \

 -b barcode.fq.gz --barcode-whitelist whitelist.txt                                       # scATAC-seq reads

./chromap --preset chip -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o aln.bed       # ChIP-seq reads

./chromap --preset hic -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o aln.pairs      # Hi-C reads and pairs output

./chromap --preset hic -x index -r ref.fa -1 read1.fq.gz -2 read2.fq.gz -o --SAM aln.sam  # Hi-C reads and SAM output

./chromap --preset chip -x index -r ref.fa -1 read1.fq -2 read2.fq -o aln.bed       # ChIP-seq reads

./chromap --preset hic -x index -r ref.fa -1 read1.fq -2 read2.fq -o aln.pairs      # Hi-C reads and pairs output

./chromap --preset hic -x index -r ref.fa -1 read1.fq -2 read2.fq -o --SAM aln.sam  # Hi-C reads and SAM output

```

## Table of Contents

@simulated.1/1

ACTCGCACGATAATCGTCATACATGGACGCGTCATTTGTTGAATACATGGTTTAATTATGAATTGCTATGGAAATCGAGAGGCCCGCTCGGTCCCCTTTA

+

IIHIIHHHIIHHIIIIGHIGGGIIEIIFEHFHIDGIDEIIIDEFGEICEBHIIIFIIHIIIBHIBE>ID>D@IICGFIBIIIB;>C7IEIIBI5GAI>IB

@simulated.2/1

CGAAACTCAAAGGATCTAGTATTGTCCATACGGCGCACACTCCGTCGGGACAACGGCATCGATGCTTACGTTAGCACCAGTTGAAGCGTGATATGTATAT

+

IIIHHIHIIHIHIIIIGIFIHFHIHIIIFHHIIIIECIEHGIHBIIBIHIIDII=GIICB>IFHIGI@FFIGHIDIFEG>:G5>A5DI<@IIIFEI@HII

@simulated.3/1

TTGCTCTCGGCAGTCTGTTTGTGGTACTATGTGCCTAGCTAATGACCTGAGAGGGTTAAGCCTTTGGATCAAGTAACGGACATACGGGGAAGATGTGACA

+

HIHHHIHIIIIHIGIIHIGIGEIGIIIIHFIG?FIGIBC@IIECHIEIIIIIII@ICFIIGCCHFFCIIIID=AEIIIIAIIE9IA=DIIIC7CIIIE7I

@simulated.4/1

ACCCACATACCGAGCTCAGGTGTGTGTGTGGAGCTACACGTAGCCAACCGTTGAGGTATACCAGGATTTCATTAATCCGAGTAATCTTGCAATAGCGCGT

+

IHIIHIHIIHHHHHGIIIFIHFIFIFIICIIIBIHIIBDAGEIIDIAGIEGHGFIIDHEIDIIIIIIIE@IDAII:BIGFIIIGC@I?IIII?IBAIIII

@simulated.5/1

CCCATGTATGTAGACGTACAAGAGAAGAGCCTGTCATTGATACCCTTGTAACTTATGCTTAAGGCCACAGATAGTGTCACGTCGACACTTCTCCTATTAC

+

HHIIHIIIHGGHIIIIHHGFHIIFFEDIIGFIIIIEAIGCIIEIIIIDEIIFCFIIIEEGIFIEIGII<?FIIGIFIIGG>D@IAAIIIII<IC@6III@

@simulated.6/1

CAGACTTGAAGCATACAGCACTGATACGGATCTGTCAGTTCGTTAGGATCGTATGTCAGCCCCGGTGTATCGCCCAACAAAATGTGTGCGCGTTCTTCTA

+

HHHIIIGIHIGHIIFGIHHEHGGFEFFICIIIIIIEFIIFCIIFIIBIIIIDIIHICIIFIIBCIDIIDIIICI@3IG9BD><IHDIII@IDE@IIII=E

@simulated.7/1

AGCGGGAGTTATAGCCGTTACTGATCGGGCATCGACACGAAGAGTCTGCGTACTGTCTTAGACGATGCTCGGTTGATTCTGACCCGAACAAGCCCGTCCA

+

HHHIIHGHIHIHIEIHHCIIHEIHHHIIIEFGIGDIIHEIIHDIIIIE?IIIBIFIIEIIIHIDIEIIAGCE>IIGI;IIAIBIIIIEFIGGI?IG<HIF

@simulated.8/1

ATATCCAGACCACGAATTTGTAACGTCCAAGTAAACCCAAGTCTGTCATAACTAAACTGTCGCAATTCTGCTAGGGTTGGACTTATGTGGTATCATTTTA

+

HIIHHIIHIIIGHIIIIHIIGGIHHIEGGIIFHHIEFIIIIIIFFEIIIIEGI?III;IIIIGDF<IIIIIIIEICICIBI@?IFIIIII?ID>CIII?H

@simulated.9/1

CGGTTGGCCCGTCGCTTACCCTTCGTAGCCAACCCGGTGGGGCCTCATCTGCGTCCTCTATTCCACCTTGGACTATAAATTTCCTTCCATGCTAGTCACT

+

IHHIIIIIHHHIIFGFIIIIHIIFGEBIIIFGIIBCIIIFAIIIIAGCAIHEIIIIFDIBI@BI@II?IF=DID@IIIIFICIIIIG@I<G=IBFEI@DC

@simulated.10/1

GGCGTGTGCAGTAAAGGGCCTAAGTCTAACGCGACAGGTGGGTTTGGCTAAGATTGCGCCTATTTGGTTTTCAAGCGGCAGTTAGTGCCCAAGGGCCGTC

+

HHIHHHIHIIHGHIDHGHHIIGGIIHEEIHEHGHEGIIIIIFDI=CHEIDFEIDIGI>IFEGIB>IIIIIFCIEIII>FAIBIA:EID<IIIIII6FGEG

@simulated.1/2

TTCCTCCTATCCTAGATGCCACTTGTGAGGCAGCGCACTACCTAACAGCTGCCACATGCCGTTGGAGTCCATAGAGGGGCGACAGTCATGTACTGCCTTA

+

HHHIIIIHGFHGIIHHIIGIEIHEHIIIIBHIFGIEIIGHIIEDIIFIFFFC<=GIIIICIIHBIIDAIIF<@I>CIIF;II45I=FFIFEIIIIB1;II

@simulated.2/2

CTTGGTAATGTCTGTCTGTCCTGTTCGCTCCTTTTGTCCTCTGGAAGTGGTTACTATAGAAGAGGCACATATGTAGAAGTTCAGGTTGGCCGGCATGTCC

+

HIIIHHIHIGHFGGIHIIIFFHIGIIEIIHIHCFIGHGBIHIIIGIAFIIEFIDEHDGHGIIIDCEIIIIFIHHIIIIIIA=IHEIIBIIIIFII=III6

@simulated.3/2

CTGTTCAAGCAGAGTCCTACCTAAGCGAAAGGTTCAGAAATGGGTGCTTAGAGTGACATAACGACATAATGAGCGCCGCTGGTCGCCCAAGGTGACGACG

+

IHIIHHIIGIIIGHEHGHIGIIFEIIHIHHHCCDGCIIIGHFIIIHEICHHIC@IHBIIBFIAIIB?IA=IEI;CIIBBHG=IIEACIHI;II8@III8I

@simulated.4/2

TCTTATATGGAATCTGGGACGTGCTGGTGGGAGCGAATCGCCCTCCACTTCACTAGGAGCACATGTGACTCCCAAACAGGGAGCTGAAGCCCACCTATGA

+

HHIIHIIIIHIGGGIHIHHIIHCHIGIICIIIEHIIGGIHIIDICEIICIIIFIIGIHI?IGIIHFII?II=IIIDIIIGFIBIGIHIB?D;IE;B:EII

@simulated.5/2

CGAGGTGCTCGGTTTCCCCACTGTCGAAGGTCCATTTGTGAATTTTCCATGATGGTACGTGGTAAATTCACTTCTTACGATAATCACCGTATTCCGTAAG

+

IIHHHHHHHIGIIIHHIIIIIIGIIGFFIHHEGGIIGGIIGIIBIIIFEBEHDIIH?IGEICIFDDIIAEIIIGIIIBFIIC85IFI=DI;?IAI@IIII

@simulated.6/2

TAGCTATACAAGTCCTACAAGTTAATATCCAAAAGCTGACAAGATTTGACATGAGCGGTCACTCCACCGCCACAGTTTCAGACACCACTGTCTATGCACA

+

HIHHHHHIHHFHIIIIEIIIHGIIGIIIGIEIHIFHGIICIHIEIFIEIIFAIICI>@IFB>IHIIHIIIIGC;E>HI:III@EICDGIICIHEI8IIDI

@simulated.7/2

GTCTATACGGTCACCGTGGACCTGCGTGTGAACACACCCGCTACTCTACAAGCACTCAACGTTTGAACTAGGCCCCCAAACGGGCGAATCTTGCGCTTTG

+

HHHHIIIHIHHIHIGHIGIFIIG@IIHEGEIIHIIIDICII@EIIHBH?DGIIEFB?IIIIIEIGIII@DHI@IIIAIIAIII@6;III;III?H=IAHH

@simulated.8/2

CCCTACACACGGTTGCAAATTCCGGCCATCTGTCTTAATAGGAGCCGTGTAGACGCATTAGATCCGAACTTTATGCTGGGTTATTCACTGCCTTAGTAAG

+

IHIIIIHIIFHIIIHIIIIIGDIIFHIHFHIGIGIIHIEDIHCII>IIGIBIFII?IICADIIIHEGI5=CIIF=IIII@;IIIAH3I88IIIIAII:II

@simulated.9/2

CCCCAGGCATCTCACCTGCTCTTACCGGTGAAGATCCAGTTCTGATACATTGGTATATGTGCGAGGTGACGACTGGCGCGATCCGGATCTTCTCATGCCC

+

IHIIIHHHIIIHGHIHIIIIGIIHIGIIIIHEICFIHCG:ICIIIIHIIGIH<EI@HII@HIIIAFBEEIIIIII>III?IF=IF8A<IIIICE9III98

@simulated.10/2

CCCAGACGCCCCGAAATTTACCCGGTCGCCGAGCAGGCTCCTGTATGGAAACAACGATGATTGCAGCGATTGTGGTGCTTCGCCCTGGTCACACCCCGAG

+

HIHHIIIGIIGHIFIIIIIIHEIIHIFHIIGGGIIIBHEFGAICIFIIHIIDEIIBCIIIABIFGIF@=IHIIIIIII<IIIAIIBCIFCIBIII;II5C