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Forum: RNA Sequencing 03-18-2014, 01:10 AM
Replies: 6
Views: 3,423
Posted By wieni
Thanks for the answers! I was also thinking...

Thanks for the answers!

I was also thinking about the local alignment. Therefore I at least tried bowtie2, but now way.

I will try 2 things:
a) new aligner - as you suggested BBMap, I would...
Forum: RNA Sequencing 03-13-2014, 11:34 AM
Replies: 6
Views: 3,423
Posted By wieni
Thanks for the answer. I am using bowtie1 as...

Thanks for the answer.

I am using bowtie1 as it is normally sad to be better when you work with short reads. I already tried bowtie2 with the whole dataset, the results are pretty different and...
Forum: RNA Sequencing 03-13-2014, 07:42 AM
Replies: 6
Views: 3,423
Posted By wieni
miRNA missed by Bowtie alignment

Hi,

I hope this question does not sound to stupid. I have the following problem. I have NGS data from miRNA sequencing. I trimm the reads, so that I have a minimum length of 16nt and a maximum...
Forum: Bioinformatics 07-04-2013, 07:00 AM
Replies: 7
Views: 8,409
Posted By wieni
ah..and correct the indention - was lost here...

ah..and correct the indention - was lost here...
Forum: Bioinformatics 07-04-2013, 07:00 AM
Replies: 7
Views: 8,409
Posted By wieni
Here a quick and dirty solution in python - was...

Here a quick and dirty solution in python - was still missing :-)


#!/usr/bin/env python

import re
import string
import sys
Forum: General 03-29-2013, 05:13 AM
Replies: 0
Views: 1,547
Posted By wieni
Generating "artificial" technical replicates of NGS data in Immunogenetics

Hi,

I hope this question has not been posted somewhere here and I haven'nt found it. In fact I would like to generate a kind of replicate dataset from an existing 454 Junior NGS dataset based on...
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