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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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REF issue #184

Closed wittney-m closed 8 months ago

wittney-m commented 8 months ago

I ran the following code but received an error message.

for f in ls -1 *_TAMA_diploidAligned.out.bam | sed 's/_TAMA_diploidAligned.out.bam//' do

miniconda3/envs/IRfinder/opt/irfinder-1.3.1/bin/IRFinder -m BAM -r /home/wdmays/intron_analysis/Emihu2data_dipl$ ${f}_TAMA_diploidAligned.out.bam

done

The error message stated: Argument error: -r intron_analysis/Emihu2data_diploid_TAMA, Does not appear to be a valid IRFinder reference. Could not find intron_analysis/Emihu2data_diploid_TAMA/IRFinder/ref-cover.bed. The reference folder contains a file name genome.fa and transcripts.gtf. The files are bam files previously aligned by STAR. What am I doing wrong? Also this is neither a human or mouse genome. Will IRfinder work for other genomes?

wittney-m commented 8 months ago

This issue has been resolved on my own.