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Forum: Bioinformatics 09-16-2015, 11:19 AM
Replies: 0
Views: 899
Posted By prepagam
problem '.' characters in multiple alignment format (MAF)

I recently downloaded the Compara.39_eutherian_mammals_EPO_LOW_COVERAGE.chr* maf (Multiple alignment format) files from ensembl.
I'm trying to process the files, and some of the software I'm...
Forum: Bioinformatics 10-25-2013, 06:36 AM
Replies: 2
Views: 2,694
Posted By prepagam
Indeed I am .. thank you for this.

Indeed I am .. thank you for this.
Forum: Bioinformatics 10-24-2013, 08:56 AM
Replies: 2
Views: 2,694
Posted By prepagam
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...
Forum: Bioinformatics 09-08-2013, 06:44 PM
Replies: 1
Views: 2,380
Posted By prepagam
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...
Forum: Illumina/Solexa 03-15-2013, 11:23 AM
Replies: 2
Views: 3,029
Posted By prepagam
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...
Forum: Bioinformatics 01-08-2013, 04:32 PM
Replies: 5
Views: 7,465
Posted By prepagam
You could also look at Scythe & Sickle. They can...

You could also look at Scythe & Sickle. They can be run independently, or added to local source galaxy.
Scythe cuts out adaptors and contamination - but never removes an entire read so your pairs...
Forum: Sample Prep / Library Generation 03-27-2012, 06:20 PM
Replies: 2
Views: 2,875
Posted By prepagam
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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