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Forum: Bioinformatics 06-25-2013, 10:47 PM
Replies: 2
Views: 2,061
Posted By Jan_R
If the directory is not in your path environment...

If the directory is not in your path environment you should put it there. This way you do not have to specify it when you type in the commands.

In .bashrc insert a new line for the directory:...
Forum: De novo discovery 11-08-2012, 03:27 PM
Replies: 3
Views: 3,015
Posted By Jan_R
I think the idea is to find artifacts in the...

I think the idea is to find artifacts in the assembly.
Any aligner that is able to open gaps should fit for this purpose. When you have aligned your assembled sequences, gaps should only be found on...
Forum: De novo discovery 11-08-2012, 12:35 PM
Replies: 3
Views: 3,015
Posted By Jan_R
I think I understand what you want to do. I...

I think I understand what you want to do. I cannot come up with a working solution but maybe TopHat can help you? http://tophat.cbcb.umd.edu/manual.html
I have never used this program but the...
Forum: Academic/Non-Profit Jobs 10-26-2012, 06:12 PM
Replies: 6
Views: 1,772
Posted By Jan_R
Good that you mention cutadapt.You can use both...

Good that you mention cutadapt.You can use both :)
I used cutadapt in combination with the FASTX tools. The FASTX Barcode Splitter seems to be not so versatile.
Forum: Academic/Non-Profit Jobs 10-25-2012, 08:44 AM
Replies: 6
Views: 1,772
Posted By Jan_R
Here are my 2 cents: 1. ... or in the...

Here are my 2 cents:

1.
... or in the dataset. When you can find exact same sequence very often in your raw data while you are checking its quality (e.g. with FastQC), it is most probably an...
Forum: De novo discovery 10-24-2012, 02:29 AM
Replies: 11
Views: 6,010
Posted By Jan_R
Seems to be Murphy's law that people are on...

Seems to be Murphy's law that people are on vacation when one comes up with questions ;)

He was specificaly interested in one specific gene so he didn't write a script for that. He just put them...
Forum: Bioinformatics 10-23-2012, 09:19 AM
Replies: 5
Views: 1,511
Posted By Jan_R
http://www.cgat.org/~andreas/documentation/pysam/u...

http://www.cgat.org/~andreas/documentation/pysam/usage.html#fetching-reads-mapped-to-a-region

Extracting reads from sam-files:
If you are familiar with python you might consider using the module...
Forum: De novo discovery 10-23-2012, 07:51 AM
Replies: 11
Views: 6,010
Posted By Jan_R
Might be a bit late but anyway: ...

Might be a bit late but anyway:
http://seqanswers.com/forums/showthread.php?t=19129

Most times the sequences in one comp(onent) do resemble each other. It is likley they are isoforms of the same...
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