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Search: Posts Made By: daniel_g
Forum: Bioinformatics 11-07-2013, 01:01 PM
Replies: 2
Views: 5,116
Posted By daniel_g
It depends on the complexity of your task, but if...

It depends on the complexity of your task, but if all you want to do is remove or rearrange columns (e.g. changing a 6-column bed to a 4-column bed) I usually find awk to be the quickest tool.

A...
Forum: Epigenetics 10-18-2013, 07:32 AM
Replies: 8
Views: 6,415
Posted By daniel_g
Okay great, thanks for the response! And yes, I...

Okay great, thanks for the response! And yes, I see what you mean. I'm not actually working with their data directly but if I were that would be a quick way to tell.
Forum: Epigenetics 10-17-2013, 11:13 AM
Replies: 8
Views: 6,415
Posted By daniel_g
Directional vs. non-directional sequencing libraries

Hello everyone,

My supervisor and I are working with bisulfite-treated whole genome sequencing data but we're having issues understanding the nuances of directional vs. non-directional libraries....
Forum: Epigenetics 09-26-2013, 11:40 AM
Replies: 10
Views: 5,767
Posted By daniel_g
The space between ":" and "p" was just to prevent...

The space between ":" and "p" was just to prevent the forum from turning it into an emoticon.

Yes, I'm using 64-bit bowtie.

Hm, that might explain why I've had fewer issues with directional...
Forum: Epigenetics 09-26-2013, 10:05 AM
Replies: 10
Views: 5,767
Posted By daniel_g
Yes, it is a shared cluster. Perhaps that's the...

Yes, it is a shared cluster. Perhaps that's the issue then.

It is indeed PBS. I understood though that if I use a command like:

qsub -l nodes=1: ppn=4

then I would get a node entirely to...
Forum: Epigenetics 09-26-2013, 09:16 AM
Replies: 10
Views: 5,767
Posted By daniel_g
Yes, I have, using the -u flag that Bismark...

Yes, I have, using the -u flag that Bismark provides for reading the first x reads. As far as I can remember this worked quite reliably.

Actually I should also mention that the jobs which are...
Forum: Epigenetics 09-26-2013, 08:55 AM
Replies: 10
Views: 5,767
Posted By daniel_g
Question Memory issues running Bismark/Bowtie alignment on a cluster

Hi all,

I'm working on aligning bisulfite converted sequence reads using Bismark and Bowtie (v1). The samples that I'm running are being aligned to the hg19 genome from UCSC. I believe that the...
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