I am trying to use
geneBody_coverage.py -r Homo_sapiens.GRCh38.97.bed -i my_file.sorted.bam -o testOutput
but it generates no results in the output. As soon as I run it, I get a wall of text that looks like this:
[NOTE:input bed must be 12-column] skipped this line: Y 26600890 26601022 ENSG00000237917 . - havana exon . gene_id "ENSG00000237917"; gene_version "1"; transcript_id "ENST00000435945"; transcript_version "1"; exon_number "12"; gene_name "PARP4P1"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "PARP4P1-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001744948"; exon_version "1"; tag "basic"; transcript_support_level "NA";
And then at the end I get this:
Total 0 transcripts loaded Cannot get coverage signal from S10nM_r1.sorted.bam ! Skip
To start with, I downloaded Homo_sapiens.GRCh38.97.gff3 from Ensembl and used gff2bed (2.4.36) to convert to a bed file which I used for reference. The first thing to do is get a 12-column bed file but I can't seem to find how to do that. But I also think I have multiple issues here and I just can't diagnose it. Any solutions?