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Search: Posts Made By: vinay427
Forum: Bioinformatics 07-20-2012, 06:44 AM
Replies: 17
Views: 4,980
Posted By vinay427
It worked perfectly! Thank you so much, it really...

It worked perfectly! Thank you so much, it really saved my day.
Forum: Bioinformatics 07-20-2012, 05:25 AM
Replies: 17
Views: 4,980
Posted By vinay427
Smile I should be thanking you! Anyway, let me try this...

I should be thanking you! Anyway, let me try this out. I'll report back soon. Thanks again!
Forum: Bioinformatics 07-19-2012, 09:31 AM
Replies: 11
Views: 3,709
Posted By vinay427
What exactly do you mean by a wrapper? From what...

What exactly do you mean by a wrapper? From what I've seen, would it basically pass through arguments to bowtie (or bowtie2) so that you can integrate it into your Python loop?

I found this...
Forum: Bioinformatics 07-19-2012, 08:58 AM
Replies: 17
Views: 4,980
Posted By vinay427
If I understand what you're saying, yes, I used...

If I understand what you're saying, yes, I used the same genome for alignment. My .diff and .fa files have both contigs and scaffolds in them, but the parts I trimmed from the top may have looked...
Forum: Bioinformatics 07-19-2012, 05:19 AM
Replies: 17
Views: 4,980
Posted By vinay427
Sent, thanks again! :)

Sent, thanks again! :)
Forum: Bioinformatics 07-18-2012, 08:07 PM
Replies: 17
Views: 4,980
Posted By vinay427
Thanks for the quick reply! In fact, I had made a...

Thanks for the quick reply! In fact, I had made a "yes" file using grep for a Python script I was trying to make. Anyway, I tried that, and after a while of working (at least more than 20 minutes) it...
Forum: Bioinformatics 07-18-2012, 09:24 AM
Replies: 17
Views: 4,980
Posted By vinay427
Hi, First of all, thanks a lot for posting...

Hi,

First of all, thanks a lot for posting this script! It is exactly what I am looking for, however I am having issues getting it working. I would try to fix it myself and post the results, but I...
Forum: Bioinformatics 07-06-2012, 11:07 AM
Replies: 11
Views: 3,709
Posted By vinay427
Anyone else feel that pbluescript's idea would be...

Anyone else feel that pbluescript's idea would be useful? I'm only trying to gain a general idea of people's opinions toward such a tool (converting .bam aligned to transcriptome and .gtf to genome...
Forum: Bioinformatics 07-05-2012, 09:26 AM
Replies: 11
Views: 3,709
Posted By vinay427
Bump, does anyone have any neat ideas or advice...

Bump, does anyone have any neat ideas or advice about a project that would be helpful to the community? Of course, it would be open-source licensed under GPL.
Forum: Bioinformatics 07-03-2012, 06:49 PM
Replies: 11
Views: 3,709
Posted By vinay427
Question Useful bioinformatics tool ideas?

Hi,

I am working at a lab for the next several weeks, and as I have strong experience in the computer side of things, I wanted to develop a tool that would be useful. My initial idea is to compile...
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