Error in creating ArrowFiles

[iremtelli1]

Hello,

I'm new to scATAC-seq analysis and trying to use this [bed file] (https://s3-us-west-2.amazonaws.com/gaulton-lab-ucsc/islet_snATAC/islet.merged.200bp_reads.bed.gz) to create ArrowFiles, however I'm getting the following error:

> ArrowFiles_HT2D <- createArrowFiles(
+   inputFiles = "/Datasets/islet.merged.200bp_reads.bed.gz",
+   sampleNames = "H_T2D",
+   filterTSS = 2,
+   filterFrags = 1000,
+   addTileMat = TRUE,
+   addGeneScoreMat = TRUE,
+   force = TRUE
+ )
Using GeneAnnotation set by addArchRGenome(Hg19)!
Using GeneAnnotation set by addArchRGenome(Hg19)!
ArchR logging to : ArchRLogs/ArchR-createArrows-2c2cf44c4c90e-Date-2021-06-24_Time-22-10-14.log
If there is an issue, please report to github with logFile!
2021-06-24 22:10:16 : Batch Execution w/ safelapply!, 0 mins elapsed.
Attempting to index /media/ag-cherrmann/itellioglu/scATAC-seq/T2D/Datasets/islet.merged.200bp_reads.bed.gz as tabix..
2021-06-24 22:10:16 : createArrowFiles has encountered an error, checking if any ArrowFiles completed..
ArchR logging successful to : ArchRLogs/ArchR-createArrows-2c2cf44c4c90e-Date-2021-06-24_Time-22-10-14.log
> ArrowFiles_HT2D
character(0)

Could you please help me with that? Thank you a lot!

[rcorces]

Your input file is not properly formatted. ArchR uses fragment files and these must be bgzipped not gzipped.

https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments

for ex.

chr1    9977    10096   CGTGGCAAGATTGACA-1      1
chr1    9988    10097   CGCACAGCAAAGGCCA-1      1
chr1    10007   10327   TAGACTGAGGGCGAAG-1      1
chr1    10013   10108   AGGCGTCTCATGTTCT-1      3
chr1    10013   10278   TAACGGTCACGCGCAT-1      1
chr1    10018   10120   TTGCAGATCCCTAAAG-1      1
chr1    10018   10151   GGGAACAAGCATGATA-1      2
chr1    10025   10125   GGAGGATCAAGGAACC-1      2
chr1    10025   10144   GTGATCAAGAGAGTAG-1      2
chr1    10026   10174   AGTTTGGGTGGACTGA-1      2

[iremtelli1]

Thank you very much! It solved my problem.

[iremtelli1]

Btw my other mistake was using hg38 instead of hg19. Maybe this helps someone else.