map a interleaved reads and orphaned reads onto assembly simultaneously, for each sample

[Former user]

Hello!

I have 24 samples, each with reads in two files: ${interleaved}.fastq and ${orphaned}.fastq. The assembly was constructed with megahit using both sets.

Correct me if I'm wrong, but to get accurate coverage statistics I need to, for each sample, map reads from the interleaved and the orphaned file onto the assembly. Can bowtie2 do that? I was thinking a one-line command for each sample, like below (no for loop here, my shell script skills are modest)

bowtie2 -p 20 -x final.contigs.build.fa --interleaved ${interleaved}.fastq -U ${orphaned}.fastq -S sample_x.sam 2> sample_x.out

[Rob Egan]

This is not a forum on how to run bowtie and we don't use that in house, so I cannot give you good advise on those parameters.

Creating a single bam file for each sample is the recommended practice for metabat so if you end up perfoming the mapping into more than one bam file, use samtools merge to bring them back into 1.