Question: Rsubread CIGAR output M only?
0
gravatar for lauren.fitch
7 weeks ago by
lauren.fitch0 wrote:

I have been using Rsubread to map reads to a short reference sequence (amplicon sequencing). The output CIGARs are in the M format rather than the X/= format. Is it possible to get Rsubread to report mismatches with X?

Thank you!

Looks like this:

> cigarbam.ms)
   [1] "239M11S"     "250M"        "250M"        "250M"        "250M"        "250M"        "250M"

I would prefer this:

> cigar(bam.pb[1:10])
 [1] "162=1X36=1X77=2X206=1X745=3X103=1X266=30X112=" "324=1X1279=30X112="                           
 [3] "125=1X17=1X822=1X637=30X110=3S"                "1740S200=1X394=1X1008=30X108=3S"   
rsubread cigar • 67 views
ADD COMMENTlink modified 7 weeks ago by Gordon Smyth39k • written 7 weeks ago by lauren.fitch0
Answer: Rsubread CIGAR output M only?
1
gravatar for Gordon Smyth
7 weeks ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

Rsubread uses the M format. You can however get the number of mismatches from the NM ("edit distance") tag: the number of Xs is NM minus any insertions or deletions.

ADD COMMENTlink modified 7 weeks ago • written 7 weeks ago by Gordon Smyth39k

Thanks, that's helpful!

ADD REPLYlink written 6 weeks ago by lauren.fitch0
Answer: C: Rsubread CIGAR output M only?
1
gravatar for Wei Shi
7 weeks ago by
Wei Shi3.2k
Australia
Wei Shi3.2k wrote:

This is something we will consider in the future development. But it is not supported at the moment.

ADD COMMENTlink written 7 weeks ago by Wei Shi3.2k
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