I am working with a species that does not have a genome sequenced. There is a partial unigene/EST database that I have used to align some Illumina RNA-Seq reads with tophat2/bowtie2. My problem is with obtaining read counts from the .bam files. Normally, I use HT-Seq but in this case I don't have a gff3 file. Our core bioinformatics director said to use custom perl scripts but that is beyond my expertise. Can anyone help?
Thanks,
Craig
Thanks,
Craig
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