Dealing with sorted bam files

[AhmedSAHassan]

Hello, I am writing here to ask if there is a way to work with sorted bam file. As I see, oarfish work only with the unsorted bam files that are generated naturally by minimap2. Since I already sorted them, are there any flag or tool to unsort them so I can quantify using oarfish?

thanks in advance.

[rob-p]

Hi @AhmedSAHassan,

I see at least two possibilities:

(1) You should be able to use samtools collate to process the file so that the records are all grouped by read name.

(2) You could convert the BAM file back into FASTQ (and make sure that there aren't duplicate entries for each read) and pass those directly to oarfish (oarfish can map the reads itself if given a FASTQ file).

In theory, both of these should work and, if done correctly, give the same results. You might try both on a small sample to ensure they agree and then do whichever is easier for you (probably (1))? Let us know if you have any follow up questions.

Best, Rob