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Search: Posts Made By: dcameron
Forum: Bioinformatics 11-01-2016, 11:09 PM
Replies: 8
Views: 5,308
Posted By dcameron
In that example can't you just take the assembled...

In that example can't you just take the assembled soft clipped bases as the consensus? If you take the final 117 bases of the assembly contig 'read'. The no-tools approach would be to right click on...
Forum: Bioinformatics 10-31-2016, 05:30 PM
Replies: 8
Views: 5,308
Posted By dcameron
Shameless plug: my structural variant caller...

Shameless plug: my structural variant caller GRIDSS (https://github.com/PapenfussLab/gridss/) performs genome-wide breakend assembly which, if you're looking for a turn-key solution to extend into...
Forum: Bioinformatics 10-31-2016, 05:15 PM
Replies: 8
Views: 5,308
Posted By dcameron
That does make sense as a simple starting point...

That does make sense as a simple starting point for filling the Ns. Code-wise, it's pretty simple and would look something like:


for each read
if cigar starts with S
replace S with...
Forum: Bioinformatics 10-30-2016, 09:35 PM
Replies: 8
Views: 5,308
Posted By dcameron
Since the read bases don't match, aren't you...

Since the read bases don't match, aren't you better off trimming the reads? What is your use case for considering mismatching bases aligned?
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