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Forum: Bioinformatics

04-19-2018, 04:49 AM

Replies: 0

BLAST taxid to complete linage using biopython on a local machine.

Views: 1,344

Posted By sublimetech

BLAST taxid to complete linage using biopython on a local machine.

Hello all,

Using BLAST, I am trying to identify thousands of sequences. To make my job a bit easier, I would like to classify these sequences first by sorting them on phylum e.g. only keep BLAST...

Forum: Bioinformatics

12-12-2014, 03:00 PM

Replies: 0

help an undergraduate with his project

Views: 1,052

Posted By sublimetech

help an undergraduate with his project

Hi,

I am an undergraduate student in bioinformatics and I am looking for some advise on a project I am working on.

I have multiple samples from a cancer. The goal is to get the lncRNA and...

Forum: Bioinformatics

11-20-2014, 06:07 AM

Replies: 13

Tophat error: Broken pipe

Views: 3,816

Posted By sublimetech

So I desided on starting runn yesterday, juse to...

So I desided on starting runn yesterday, juse to so what would happen if I provided less inputs. Here is the output:

[2014-11-19 13:33:33] Beginning TopHat run (v2.0.9)...

Forum: Bioinformatics

11-19-2014, 10:52 AM

Replies: 13

Tophat error: Broken pipe

Views: 3,816

Posted By sublimetech

I do, Also could you explain why biological...

I do, Also could you explain why biological replicates need to be done in separate runs as opposed to one run for technical replicates? (need to put everything in a report for school)

Forum: Bioinformatics

11-19-2014, 09:53 AM

Replies: 13

Tophat error: Broken pipe

Views: 3,816

Posted By sublimetech

Biological replicates. so what I gather the...

Biological replicates. so what I gather the mentioned link is that I should run tophat 50 times? (once for each paired read)

Forum: Bioinformatics

11-19-2014, 09:32 AM

Replies: 13

Tophat error: Broken pipe

Views: 3,816

Posted By sublimetech

but doesnt the command require a list?

but doesnt the command require a list?

Forum: Bioinformatics

11-19-2014, 08:54 AM

Replies: 13

Tophat error: Broken pipe

Views: 3,816

Posted By sublimetech

I am specifying all 100 files and running in a...

I am specifying all 100 files and running in a terminal

Forum: Bioinformatics

11-19-2014, 08:39 AM

Replies: 13

Tophat error: Broken pipe

Views: 3,816

Posted By sublimetech

Tophat error: Broken pipe

Hi,

I am a student trying my hand at bioinformatics. While performing an analysis I got the following output:

[2014-11-04 11:54:56] Beginning TopHat run (v2.0.9)...

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