Question: Help Understanding bamtobed Flag -split
gravatar for Viz
15 months ago by
Viz40 wrote:

Hello, as the title states I just need a little help fully understanding what the -split flag does in the bedtools utility, bamtobed. It states,

-split Report each portion of a “split” BAM (i.e., having an “N” CIGAR operation) alignment as a distinct BED intervals.

However, upon being asked about how this affects output I couldn't properly answer(It gives us expected results when used, when it is missing the results are wrong). I was wondering if someone could help me understand what exactly happens with this flag.

Link to bamtobed manual

rna-seq sequence • 275 views
ADD COMMENTlink modified 15 months ago by Pierre Lindenbaum134k • written 15 months ago by Viz40
gravatar for Pierre Lindenbaum
15 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

if you have a cigar string like this: 10M100N20M : the tool will break your record in two lines; one bed line of 10 bases (10M) and another one of 20 bases (20M), ignoring the 'intron' of 100 bp

ADD COMMENTlink written 15 months ago by Pierre Lindenbaum134k

That's what I assumed but I just wanted to be sure, thank you so much! Accepted.

ADD REPLYlink written 15 months ago by Viz40
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