[GenoMax]

Yep - "trd" can be used on the fasta file prior to mapping, or the parameter "trd" can be added during mapping. However, once the reads are mapped, Reformat will not change the "rname" field of the sam file, just the "qname". That's a good idea, though - I'll change it so that it can do that.

If you are going to add that is there a way to make it act only on the genome name (with a new option name for reformat).

I would not want to lose the R1/R2 information in read headers, if trd takes out all things after first space.

[Brian Bushnell]

If you are going to add that is there a way to make it act only on the genome name (with a new option name for reformat).

I would not want to lose the R1/R2 information in read headers, if trd takes out all things after first space.

Unfortunately, the sam specification does not allow retaining R1/R2 information anyway, because R1 and R2 are required to have the same name. You can override this in BBMap with the flag "keepnames", which I find very helpful in a lot of situations, but bear in mind that the result is not a spec-compliant sam/bam file.

Currently, "trd" in BBMap trims after the whitespace for both reads and ref sequences. I guess I could add an option to do them independently, and a similar flag for Reformat.

[chiayi]

@Brian, @GenoMax,
Thanks for all the clarification. It's very helpful.
It turned out my original issue was solely caused by the descripancy in the genome name. The latest version of featureCounts can recognize CIGARs from samtools v1.4. I heared that from Wei and did a test run. It worked.

[Brian Bushnell]

Great to hear; thanks!