BenLangmead
commented
1 year ago I am unsure how to answer the question as bowtie2 does not itself output any kind of count table. It must be that the count table you are asking about is something output by another tool that runs after bowtie2, like featureCounts or similar.
TJrogers86
Hello developer,
I dont think this is a question that has been asked in the issue section, but if so please direct me there. If not, I have some viral contigs that I used bowtie2 to map reads back to. I can normalize these reads by converting to TPM. However, I have been reading about the effects of different normalization on alpha and beta diversity matrix. Historically, when working with amplicon libraries, we tend to rarify the counts. I know currently this practice is frowned upon. But, just to see the effect, I would like to rarefy my count table for these contigs. They range in length from 1,000 bp to 300,000 bp. My question is does bowtie2 account for the length of the sequence when creating its count table? If not, then I think will need to account for the length before I rarefy. Any information would be greatly appreciated.