Forum: Bioinformatics
09-16-2015, 11:19 AM
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Replies: 0
Views: 899
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Forum: Bioinformatics
10-25-2013, 06:36 AM
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Replies: 2
Views: 2,694
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Forum: Bioinformatics
10-24-2013, 08:56 AM
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Replies: 2
Views: 2,694
remove soft-clipped bases
I need to conduct some computations using a python script directly on some BWA aligned bam files.
For this, I need to remove the soft clipped bases. i.e. if the cigar string and read is: 2S8M...
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Forum: Bioinformatics
09-08-2013, 06:44 PM
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Replies: 1
Views: 2,380
Coordinate sorted sam
I need to create a galaxy only pipeline for a course which trims, aligns then calls variants in GaTK.
I aligned with BWA, but cannot proceed further as the sam file is coordinate unsorted...
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Forum: Illumina/Solexa
03-15-2013, 11:23 AM
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Replies: 2
Views: 3,029
Lib prep - Splitting PCR to reduce PCR bias
I want to reduce my high levels of duplicate reads (>50%) in my illumina HiSeq 100bp Paired end sequences.
The normal solutions aren't possible as I am using the max DNA available per sample...
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Forum: Bioinformatics
01-08-2013, 04:32 PM
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Replies: 5
Views: 7,465
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Forum: Sample Prep / Library Generation
03-27-2012, 06:20 PM
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Replies: 2
Views: 2,875
Bioruptor - DNA in TE?
Various protocols for bioruptor shearing suggest that you reconstitute your DNA to your desired concentration in TE (e.g. 1ug DNA in 100ul TE). My DNA samples were eluted in Qiagen's AE elution...
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