Forum: Bioinformatics
12-27-2014, 07:26 AM
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Replies: 0
Views: 1,539
Quantify similarity between multi-fasta files
Hi there,
I want to compare the output of de novo assemblies of multiple samples. From this, I'd like to cluster the samples on (dis)similarity.
With bla(s)t, I get per-sequences scores (which...
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Forum: Bioinformatics
10-17-2014, 02:28 PM
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Replies: 0
Views: 1,010
Quantifying copies of a single locus
Hi all,
I'm trying to count to number of repeating elements in a genome (the locus of interest has a variable number of copies). Trying to keep it simple has led me to count mapped NGS-reads to an...
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Forum: Bioinformatics
06-21-2014, 11:22 AM
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Replies: 1
Views: 4,079
Some chromosomes missing in bwa-output
Hello!
I have fasta-files, resulting from a de novo assembly. When I map pe-reads to these fastas with bwa-mem (default options), it does not output all the fasta-entries: when looking at the...
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Forum: Bioinformatics
11-27-2013, 03:25 AM
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Replies: 2
Views: 1,940
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Forum: Bioinformatics
11-25-2013, 12:00 AM
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Replies: 2
Views: 1,940
Extracting readnames from pindel
Hi everybody, very short question:
Is there a possibility to get the 'mapped' readnames from pindel?
In that way, one could extract those reads from the unmapped-read pool.
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Forum: Bioinformatics
09-16-2013, 06:13 AM
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Replies: 1
Views: 2,527
I found help from one of our perl-wizards and,...
I found help from one of our perl-wizards and, although quick 'n dirty, there is a solution. I hope someone else can benefit and/or learn from this. It prints out the summaryline and its reads, when...
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Forum: Bioinformatics
09-16-2013, 05:05 AM
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Replies: 1
Views: 2,527
Filtering DELLY output
I have an output of DELLY which looks like this:
HMR:ERR007538.3275891 83 1 9695 35 = 9437 -294 Library0
HMR:ERR007571.842092 99 1 ...
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Forum: Bioinformatics
09-16-2013, 05:01 AM
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Replies: 2
Views: 8,928
I would check the FastX toolskit, which has a...
I would check the FastX toolskit, which has a renamer-tool in it: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html.
Edit: http://www.biostars.org/p/68477/ has more options for renaming...
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Forum: Introductions
09-16-2013, 04:53 AM
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Replies: 0
Views: 946
Hello from Holland!
Hi there, my name is Robin and I'm in the Cancer Genomics & Developmental Biology masters programme of Utrecht University. I have a BSc in biology, with a focus on systems- and genome-biology. The...
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