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Search: Posts Made By: danielecook
Forum: Bioinformatics 10-16-2013, 06:14 PM
Replies: 8
Views: 3,759
Posted By danielecook
Yeah - I am taking care to verify that things...

Yeah - I am taking care to verify that things look correct in IGV as far as build is concerned. The past folks were confident its mm9. I will for sure look into useq. Greatly appreciate all your...
Forum: Bioinformatics 10-16-2013, 12:25 PM
Replies: 8
Views: 3,759
Posted By danielecook
This was a project that was passed on to me. It's...

This was a project that was passed on to me. It's a ChIP-seq experiment. We are hoping to compare our data against another groups ChIP-seq work which was comparable but in a different cell line. We...
Forum: Bioinformatics 10-16-2013, 11:45 AM
Replies: 8
Views: 3,759
Posted By danielecook
Unfortunately - this is the only file I was given...

Unfortunately - this is the only file I was given to work with. I guess the quality scores were truncated before I got to this? Not sure...

Thanks for your help. Do you know if there are any tools...
Forum: Bioinformatics 10-16-2013, 10:42 AM
Replies: 8
Views: 3,759
Posted By danielecook
I suspect the names have changed - here is a...

I suspect the names have changed - here is a sample of the file:



The file name is simply ends in '.extended'
Forum: Bioinformatics 10-15-2013, 11:55 AM
Replies: 8
Views: 3,759
Posted By danielecook
Smile eland extended

I've been given some 'eland extended' files to work with. There really isn't much online about these. I'm trying to convert them to sam/bam format or something more useful but I keep hitting dead...
Forum: Events / Conferences 10-13-2013, 09:51 AM
Replies: 4
Views: 5,423
Posted By danielecook
Smile Thanks for the tips

I appreciate the feedback. We do have a supercomputer here I can make use of, and I do have some experience with Amazon in the cloud.

Actually - the data I am working with is already aligned...
Forum: Introductions 10-12-2013, 10:36 AM
Replies: 0
Views: 1,473
Posted By danielecook
Smile Greetings

Hi - I am a grad student at Northwestern.
Forum: Events / Conferences 10-12-2013, 10:13 AM
Replies: 4
Views: 5,423
Posted By danielecook
Hi - I've got a question regarding using...

Hi -

I've got a question regarding using Bioconductor. I've been struggling with Bioconductor for the past week - I was under the impression that Bioconductor could be used for 'high-throughput'...
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