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Forum: Academic/Non-Profit Jobs 10-09-2015, 10:12 AM
Replies: 0
Views: 699
Posted By duane.hassane
Cancer Genomics Research Specialist Position Available, Weill Cornell, New York City

We're hiring talented scientists in the cancer genomics laboratory of Dr. Duane Hassane (http://drduanehassane.com/blog) at Weill Cornell Medical College in Manhattan. The laboratory focuses on...
Forum: Bioinformatics 06-11-2015, 10:47 AM
Replies: 212
Views: 57,083
Posted By duane.hassane
Ok. Will take a look at this approach. Thank...

Ok. Will take a look at this approach. Thank you!
Forum: Bioinformatics 06-11-2015, 10:18 AM
Replies: 212
Views: 57,083
Posted By duane.hassane
Yes, bbduk with restrictright and/or restrictleft...

Yes, bbduk with restrictright and/or restrictleft set to constrain the search to the ends where primers are located. This is actually extremely fast and efficient even with hundreds of primers. ...
Forum: Bioinformatics 06-11-2015, 09:44 AM
Replies: 212
Views: 57,083
Posted By duane.hassane
Thanks. To be more clear, I am after removing...

Thanks. To be more clear, I am after removing the primers themselves (either from the fastq or BAM) and preserving the intervening sequence only. In this use case, there are hundreds of different...
Forum: Bioinformatics 06-11-2015, 04:58 AM
Replies: 212
Views: 57,083
Posted By duane.hassane
Is there a way of efficiently using the BBMap...

Is there a way of efficiently using the BBMap tools to cut variable length and variable sequence primer pairs from amplicon sequencing data either pre-alignment (fastq) or post-alignment (BAM)? I am...
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