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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Error! 635104 Cannot Convert to int #97

Closed tzvi909 closed 1 year ago

tzvi909 commented 1 year ago

Hi,

Wanting to use this for my ATAC-seq peak calling pipeline but can't quite seem to get it to work on my bam files.

Have already pre-sorted my bam files using samtools sort -n and when running the following code, it comes up with "Error! 635104 cannot convert to int". Do you know how I can fix this?

for prefix in $(ls *.sorted-readnames.bam); do echo "calling peaks in $prefix"; Genrich -t ${prefix%.*.*}.sorted-readnames.bam \ -o ${prefix%.*.*}.narrowPeak \ -b ${prefix%.*.*}_peaks.bed \ -e MT -E /rds/homes/d/daviesjp/.nextflow/assets/nf-core/atacseq/assets/blacklists/GRCh38_v3.bed \ -p 0.05 -j ; done

Cheers

tzvi909 commented 1 year ago

These files have worked with MACS2 and HMMRATAC btw so not sure what's going on.

tzvi909 commented 1 year ago

Nevermind. Solved by putting chr before all chromosome numbers in the blacklist file.