Extract Hard-clipped and soft-clipped values from fifth column
Hello all,
Is it possible to know how I can extract 105 hard-clipped base from fifth column and then add value 105 to end coordinate of chr1 ?
As I tried with awk, but no success !
chr1 21730812 21730857 M00758:777:BKR4B:1:2103:25646:13282 45M105H
chr1 179196680 179196716 M00758:777:BKR4B:1:2101:24687:24458 87H36M27H
Thanks a lot!
• 2,605 views
•
link
updated
by
Pierre Lindenbaum
•
written
by
Ram
•
written
by
Ram
0 answers
No answers yet.
Log in to answer this question.
show us the awk code
do you really want to do this ??? how would you handle a 'N' or a 'D' in the cigar string ???
Here is the code :
can you please explain this awk script ?
This is your input :
And you want a result like this :
?
I want a result like this :
Thanks !
You wish to add number of Matched based to start position and number of hard clipped to end position?
Why?
You mean for the first line :
Because
45M105Hdoes not have hard clipping as startYes ! Any idea how i can be able to achieve this ?
Please explain your awk script as it does nothing to pick relevant parts of
$5or add to$2or$3. I don't even see why a loop is necessary in your awk script.Also, please edit your question and add your awk script in there.
What is the larger problem that you are attempting to solve, and why only hard clips, not soft clips?
Wouldn't it be easier to just use a utility such as
gridss.ComputeSamTags SOFTEN_HARD_CLIPS=trueto convert your hard clips into soft clips then do you conversion to BED?Hello Ram,
Please provide feedback to the comments here so we can get this discussion to closure.
Thank you!