what does X means in bam2R result of deepSNV package?
1
0
Entering edit mode
@thestaroceanster-10072
Last seen 4.2 years ago

 

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 • 778 views
ADD COMMENT
1
Entering edit mode
@storybenjamin-11722
Last seen 7 months ago
Germany

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 COMMENT
0
Entering edit mode

Thanks, that definitely solved that!

ADD REPLY

Login before adding your answer.

Traffic: 642 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6