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Forum: Bioinformatics 09-01-2014, 11:51 PM
Replies: 2
Views: 2,116
Posted By kokonech
Qualimap (http://qualimap.org) outputs percentage...

Qualimap (http://qualimap.org) outputs percentage of reads in intronic and intergenic regions as one of the quality metrics for RNA-seq data.
Example report can be found here...
Forum: Bioinformatics 07-22-2014, 08:32 AM
Replies: 9
Views: 1,414
Posted By kokonech
You should check out QualiMap, which is useful to...

You should check out QualiMap, which is useful to get an overview of BAM file:
http://qualimap.bioinfo.cipf.es/

It computes plenty of useful quality metrics such as mean and std coverage,...
Forum: Bioinformatics 07-14-2014, 05:26 AM
Replies: 1
Views: 1,059
Posted By kokonech
Hi Alex! According to the manual, the values...

Hi Alex!

According to the manual, the values --min-coverage-intron and --max-coverage-intron are used only when --coverage-search option is activated. This is a special mode for Tophat, which uses...
Forum: Bioinformatics 09-19-2013, 11:30 PM
Replies: 6
Views: 3,961
Posted By kokonech
Hi! Make sure the BAM file is sorted by...

Hi!

Make sure the BAM file is sorted by coordinate and the splitted alignment is defined by N cigar code (true for tophat by default).

Also you might check some alternative ways to calculate...
Forum: Bioinformatics 09-03-2013, 04:52 AM
Replies: 2
Views: 1,626
Posted By kokonech
One possiblity is to search for gene fusions and...

One possiblity is to search for gene fusions and other transcriptome rearrangements.
There are tools out there which are targted on this like for example deFuse...
Forum: RNA Sequencing 08-08-2013, 03:01 AM
Replies: 1
Views: 1,557
Posted By kokonech
Hi! Well, as far as I know, usually...

Hi!



Well, as far as I know, usually dashes are used in sequence alignment visualization to represent gaps (http://www.bioinformatics.org/wiki/Sequence_alignment).



One explanation for...
Forum: RNA Sequencing 08-08-2013, 02:39 AM
Replies: 1
Views: 1,211
Posted By kokonech
Hi, I suppose potential_fusion.txt is an...

Hi,

I suppose potential_fusion.txt is an intermideate file. According to tophat-fusion documenation you should look on files result.txt or result.html, which contains the results. More details are...
Forum: Bioinformatics 05-10-2013, 12:59 AM
Replies: 2
Views: 2,308
Posted By kokonech
The protocol strand-specificity is well-explained...

The protocol strand-specificity is well-explained in this post:
http://onetipperday.blogspot.de/2012/07/how-to-tell-which-library-type-to-use.html

According TopHat FAQ the library information is...
Forum: Bioinformatics 01-09-2013, 07:59 AM
Replies: 40
Views: 17,261
Posted By kokonech
Hi, does anybody have a response from the...

Hi,
does anybody have a response from the authors or any clues how the filtering of juncions.out occur?

In my simulation experiments I have a large list of fusion candidates (about 500), and...
Forum: Bioinformatics 04-20-2011, 09:19 PM
Replies: 4
Views: 1,731
Posted By kokonech
Evaluation of asssembly algorithms ...

Evaluation of asssembly algorithms
http://gage.cbcb.umd.edu/

BTW, MIRA3 is de novo assembly, while Bowtie is short read aligner. Not sure, but I think Geneious use their own algorithm.
Forum: Bioinformatics 04-03-2011, 08:06 PM
Replies: 2
Views: 3,111
Posted By kokonech
Why not use an external filter? For example, here...

Why not use an external filter? For example, here (http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc214)'s a simple Biopython scirpt to filter reads that have quality below some fixed...
Forum: Bioinformatics 04-03-2011, 08:00 PM
Replies: 6
Views: 4,664
Posted By kokonech
There is an open source genome analysis suite...

There is an open source genome analysis suite called UGENE (http://ugene.unipro.ru). You should give it a try. It has a lot of capabilities to manage annotations.

From your wish-list it supports...
Forum: Bioinformatics 03-28-2011, 08:51 AM
Replies: 3
Views: 4,217
Posted By kokonech
You can use UGENE (http://ugene.unipro.ru)...

You can use UGENE (http://ugene.unipro.ru) extension Workflow Designer.

I've attached a workflow schema that allows to input multiple genbank files and merge them into single one.

Install...
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