Paired-end to Single-end


I have a bam file that is paired ended.

I'm told our pipeline only uses single-end (R1 only). How could I pull only the R1 reads from the bam?



You seem unsure on which processing was applied to your original data. You know, you can view the commands used by looking at the BAM [SAM] header:

samtools view -H myalignment.bam ;

The last command used will appear at the bottom of the header (or should appear, at least). Please share here, if you wish.

Otherwise, there are many commands available to convert a BAM to FASTQ. Please see:

With these commands, one can control output of R1 and R2. In your case, we seem to not have 100% certainty about which was aligned, though. This will be revealed by observing the header, as mentioned above.


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