Hello community. I'm new to sequence analysis with SeqMonk and I must be doing something wrong because the software is ignoring mitochondrial RNA reads in SubRead RNA-seq output BAM files. I did find the instructions for placing an alias file in the same folder as the genome build but I still can't get it to work. I always get a 'couldn't extract valid data from chrM' error for each skipped entry. I'm assuming that SubRead uses the 'chrM' convention when mapping reads, so is it just the syntax or string in the alias file that I've got wrong? I can't look into the BAM files to check for myself.
Can someone tell what the correct string to use is?
Should it be chrM MT? (tab delimited) If so, that didn't work for me.
Sorry if this sounds a bit thick. I'm actually interested in the mitochondrial reads!
TIA David
Can someone tell what the correct string to use is?
Should it be chrM MT? (tab delimited) If so, that didn't work for me.
Sorry if this sounds a bit thick. I'm actually interested in the mitochondrial reads!
TIA David
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