Question: what does X means in bam2R result of deepSNV package?
0
gravatar for thestaroceanster
3 months ago by
thestaroceanster0 wrote:

 

Currently I am working with deepSNV and realized that the bam2R output results with A T C G X and N. I am aware of N stands for the reads that did not meet the threshold of quality, but I could not figure out what X stands for? I check the manual and the other information about it might be it stands for '-', but the insertion and deletion are provided in  (INS)ertions, (DEL)etions columns. So what does X means in bam2R result?

deepsnv • 126 views
ADD COMMENTlink modified 3 months ago by story.benjamin10 • written 3 months ago by thestaroceanster0
Answer: what does X means in bam2R result of deepSNV package?
1
gravatar for story.benjamin
3 months ago by
story.benjamin10 wrote:

When I run the program I get the following column names in the output from bam2R

   A    T    C    G  -   N  INS DEL HEAD TAIL   QUAL

 

The "-" represents gaps (so it may be present for spliced alignments; e.g. introns). 

My guess is you converted the output to a data.frame which renamed that column to "X.".

ADD COMMENTlink modified 3 months ago • written 3 months ago by story.benjamin10

Thanks, that definitely solved that!

ADD REPLYlink written 12 weeks ago by thestaroceanster0
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