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Forum: Bioinformatics 12-27-2014, 07:26 AM
Replies: 0
Views: 1,539
Posted By robinweide
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...
Forum: Bioinformatics 10-17-2014, 02:28 PM
Replies: 0
Views: 1,010
Posted By robinweide
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...
Forum: Bioinformatics 06-21-2014, 11:22 AM
Replies: 1
Views: 4,079
Posted By robinweide
Question 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...
Forum: Bioinformatics 11-27-2013, 03:25 AM
Replies: 2
Views: 1,940
Posted By robinweide
Ah okay, didn't scrolled all the way to the right...

Ah okay, didn't scrolled all the way to the right of your example output.

Another question: the CloseEndMapped- file... Are those the (former unmapped) reads, that are now split-mapped? And what...
Forum: Bioinformatics 11-25-2013, 12:00 AM
Replies: 2
Views: 1,940
Posted By robinweide
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.
Forum: Bioinformatics 09-16-2013, 06:13 AM
Replies: 1
Views: 2,527
Posted By robinweide
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...
Forum: Bioinformatics 09-16-2013, 05:05 AM
Replies: 1
Views: 2,527
Posted By robinweide
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 ...
Forum: Bioinformatics 09-16-2013, 05:01 AM
Replies: 2
Views: 8,928
Posted By robinweide
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...
Forum: Introductions 09-16-2013, 04:53 AM
Replies: 0
Views: 946
Posted By robinweide
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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