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ylab-hi / ScanExitron

A computational workflow for exitron splicing identification
MIT License
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regtools junctions annotate error #11

Closed macoreL closed 1 week ago

macoreL commented 1 year ago

Hi, some errors happened when i used Scanexitron. The snapshot was shown: 1688395078558 Scanexitron can run successfully using test data. I only change the reference genome for my data. The command "cat Homo_sapiens.GRCh38.109.gtf | awk 'OFS="\t" {if ($3=="CDS") {print $1,$4-1,$5,$10,$20,$7}}' | tr -d '";' > Homo_sapiens.GRCh38.109.CDS.bed " was used to generate CDS file. could you please tell me what is wrong and how to fix this? Thank you

nttg8100 commented 3 months ago

I had similar issue, then I found that the error may come from the fasta file, gtf file. It is quite early at the beginning of the chromosome so we may have so many NNNNNNN then it failed to extract I guess. I got this issue on the chromosome 10. As a result, I change to use the gtf gencode v37, hg38 from ucsc for fa. It solved the issue.