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Forum: RNA Sequencing 08-18-2011, 05:41 AM
Replies: 0
Views: 925
Posted By abakelaar
SNVannotator

hello

can anyone tell me how I can do this option:

The current version includes a set of reference resources required for hg18. More genomes and versions will be added.

A resource.cfg file...
Forum: RNA Sequencing 08-16-2011, 05:52 AM
Replies: 1
Views: 1,249
Posted By abakelaar
SNVmix pileup2matlab.pl

hello

Is there anyone who knows about the perl script pileup2matlab.

I cant find it anywhere

gr
Forum: RNA Sequencing 08-04-2011, 04:55 AM
Replies: 1
Views: 3,253
Posted By abakelaar
mapping with gmap

Hi there

I'm trying to map data with gmap. It runs, but it takes hours:rolleyes:.
he prints a message: no paths found for .... is this good or bad???
I've got paired-end files with each 6 gb ...
Forum: Introductions 07-27-2011, 11:50 PM
Replies: 5
Views: 1,858
Posted By abakelaar
Ik loop stage voor Kees Tensen afdeling huid. dus...

Ik loop stage voor Kees Tensen afdeling huid. dus dat is niet echt een bio-informatica afdeling maar ik word goed geholpen door de afdeling lgtc, waar Johan den Dunnen volgens mij ook werkt.
...
Forum: RNA Sequencing 07-27-2011, 11:14 PM
Replies: 0
Views: 1,582
Posted By abakelaar
snvmix

hi there


is there anybody who have experience with snvmix

greetings anneke
Forum: Introductions 07-27-2011, 10:44 PM
Replies: 5
Views: 1,858
Posted By abakelaar
hey marten, Ik loop nu stage aan het lumc,...

hey marten,

Ik loop nu stage aan het lumc, daar ben ik bezig met RNA-seq data te analyseren. het is best lastig:) En bevalt je werkplek bij baseclear en waar werk jij dan aan?

groetjes anneke
Forum: RNA Sequencing 07-27-2011, 04:11 AM
Replies: 0
Views: 1,653
Posted By abakelaar
differences between seattleseq and annovar

what are the differences between seattleseq and annovar.
Forum: RNA Sequencing 07-27-2011, 12:38 AM
Replies: 2
Views: 1,769
Posted By abakelaar
auto_annovar

can anyone tell me what's wrong


[abakelaar@iPipeline annovar]$ perl auto_annovar.pl -model recessive 0004_61WDG_s_5 humandb/hg18/ --buildver hg18 ...
Forum: RNA Sequencing 07-27-2011, 12:28 AM
Replies: 0
Views: 2,148
Posted By abakelaar
tutorial annovar

hello

is there somebody who can tell me which steps I need to do in annovar.

I want filtering mutations who are damaging the gene. so would I take the 3 steps with all databases en at least...
Forum: Introductions 07-27-2011, 12:22 AM
Replies: 5
Views: 1,858
Posted By abakelaar
Bio-informatics student

Hello Im Anneke Bakelaar

Im a student bio-informatics at HS leiden. I'll work on RNA-seq data and i''ll get target genes.
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