what does X means in bam2R result of deepSNV package?
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@thestaroceanster-10072
Last seen 4.5 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 • 846 views
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@storybenjamin-11722
Last seen 10 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.".

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Thanks, that definitely solved that!

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