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Forum: Bioinformatics 11-02-2016, 06:50 AM
Replies: 8
Views: 3,938
Posted By dayhan
As a starting point, yes, I'm trying manual...

As a starting point, yes, I'm trying manual editing. But there are more than 1000 instances, and I was thinking to automate the process.

Thank you for your responses.
Forum: Bioinformatics 11-01-2016, 09:23 AM
Replies: 8
Views: 3,938
Posted By dayhan
Thank you for your response. I can see the...

Thank you for your response. I can see the soft-clipped parts in IGV and they can be assembled cleanly in most cases (attached). I am not good with programming but I can try what you suggested.

...
Forum: Bioinformatics 10-27-2016, 11:23 AM
Replies: 8
Views: 3,938
Posted By dayhan
replacing CIGAR string

Hello,

I want to replace the CIGAR strings of SAM/BAM file without changing anything else so that the soft-clipped bases are shown as matches/mismatches.

e.g. 11S60M becomes 71M
15M1D40M15S...
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