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I have a collapsed fasta files with all my counts and the corresponding sequences. I would like to annotate those sequences onto a gff file to find out what they are. Is this possible? Usually I would need a bam/sam file, but I dont have that for these sequences.
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So map the collapsed fasta file to something and then count accordingly. Just make the counts part of the read name so you can get them back later. BTW, you made your life more difficult by collapsing things like that. Aligners are fast enough these days to handle whatever size data you want to throw at them.
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