Bowtie2 alignment on metagenomics - sum same sequence

Question

[rfour92]

Hello,

I have multiple metagenomic assemblies. I have obtained the ffn file of the orfs, then merged them together and clustered them using cd-hit-est. when I use bowtie2 to map these sequences against reads, bowtie2 records multiple mappings (as it should) however it saves them under the same sequence header. I only care about the total count of each sequence. So i was wondering is there a way where I can ask bowtie2 to sum up the total hits per sequence? Or do I need to use another tool to perform this task? Kindly advise.

Thank you

Answer 1

[Buffo]

I use bowtie2 to map these sequences against reads

You should do exactly the opposite, map reads against your consensus sequences. Then you can use samtools idxstats to count the reads mapped.

[rfour92]

Thanks, i highly appreciate your reply. I have been stuck for few weeks now. I will give it a shot as soon as I can