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CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
https://reg-gen.readthedocs.io/
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IndexError: index is out of bounds #272

Closed sathvik-samaga closed 1 month ago

sathvik-samaga commented 1 month ago

Hi, I am trying to get differential peaks using RGT-THOR and This is what my THOR.config file looks like -

rep1

treated_ATAC_sorted.bam

rep2

untreated_ATAC_sorted.bam

chrom_sizes

GRCh38_EBV.chrom.sizes.tsv

I downloaded the chromosome size file from encode as I used the reference genome from encode for my alignment, this is the code im using - 

rgt-THOR THOR.config -n ATAC  --report

I keep getting this error - "IndexError: index -1 is out of bounds for axis 0 with size 0" my chromosome file looks fine and im sure my bam files are not corrupt. Any help in resolving this error would be appreciated, thanks.