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Forum: Bioinformatics 12-12-2012, 02:16 AM
Replies: 52
Views: 17,328
Posted By stoker
Dear all, Currently we try to run pBWA on our...

Dear all,
Currently we try to run pBWA on our cluster as well.

Unfortunately, we have problems with proper index generation. I suppose pBWA index differs from bwa one - there is an additional...
Forum: Bioinformatics 03-04-2012, 11:52 PM
Replies: 21
Views: 16,626
Posted By stoker
Dear all, I am working on short RNA sequencing...

Dear all,
I am working on short RNA sequencing already for some time. I can agree with Simon Anders, that RNA-Seq is linear and DEseq or TMM are good solutions. On the other hand our experience is...
Forum: Bioinformatics 10-02-2011, 01:55 AM
Replies: 16
Views: 11,847
Posted By stoker
Since you have only 2 samples, I think there is...

Since you have only 2 samples, I think there is no place for statistics - you can not discuss about any population phenomena just on the base of 2 samples. What you can do best in my opinion is just...
Forum: Bioinformatics 10-01-2011, 11:43 AM
Replies: 16
Views: 11,847
Posted By stoker
It would be nice if you could write the number of...

It would be nice if you could write the number of samples you have - then it would be easier to say if the test you apply is proper. Differential fpkm analysis does not take much time - similarly as...
Forum: Events / Conferences 09-28-2011, 09:50 PM
Replies: 1
Views: 1,947
Posted By stoker
Genome Informatics at CSHL - anyone planning to go?

As in topic - anyone planning to go for this event?
Forum: Bioinformatics 08-16-2011, 01:13 AM
Replies: 10
Views: 12,420
Posted By stoker
What about the case if my pair end fastq files...

What about the case if my pair end fastq files have different number of reads (Illumina GAIIx)? Could you suggest any software to find common part?
Forum: Bioinformatics 07-27-2011, 09:54 PM
Replies: 10
Views: 6,528
Posted By stoker
You need to login as root (su command).

You need to login as root (su command).
Forum: Bioinformatics 07-07-2011, 12:53 AM
Replies: 0
Views: 1,004
Posted By stoker
Fastq sorting and common part?

Dear community,
I have 3 huge fastq files for paired end multiplexed read:
I would like to extract from them the common part, so clusters for which I have both reads and multiplexing index. I would...
Forum: Bioinformatics 05-22-2011, 11:31 PM
Replies: 13
Views: 3,807
Posted By stoker
I have observed that Illumina instruments have...

I have observed that Illumina instruments have different filters configurations. If your filters has been mounted incorrectly - in wrong positions (this is possible when you have a new device or you...
Forum: Bioinformatics 05-06-2011, 03:21 AM
Replies: 31
Views: 11,689
Posted By stoker
Dear all, FPKM calculation with 0.9.3 and 1.0.0...

Dear all,
FPKM calculation with 0.9.3 and 1.0.0 gives significantly different results. The best genes on our cancer samples had FPKM of approx. 15000, now this values changed to ~1.5M. Whats more,...
Forum: Bioinformatics 04-07-2011, 12:57 PM
Replies: 10
Views: 6,528
Posted By stoker
Solved, Enter the /bin directory, and create...

Solved,
Enter the /bin directory, and create there a soft link to bowtie (Bowtie will become a system command)
You can make it with ln -s /your/path/to/bowtie/bowtie bowtie
Forum: Bioinformatics 04-04-2011, 02:43 AM
Replies: 2
Views: 1,785
Posted By stoker
This may be useful: Genomics. 2010...

This may be useful:

Genomics. 2010 Nov;96(5):316-21. Epub 2010 Aug 13.
Pokrzywa R, Polanski A.; BWtrs: A tool for searching for tandem repeats in DNA sequences based on the Burrows-Wheeler...
Forum: Bioinformatics 03-28-2011, 03:55 AM
Replies: 17
Views: 24,972
Posted By stoker
I have reversed problem - my bowtie runs well...

I have reversed problem - my bowtie runs well with reference name (ex. hg19) but does not work with the full path of indexes, which I need for my local Galaxy.

This does not work:
bowtie -q -p 4...
Forum: Bioinformatics 03-28-2011, 03:47 AM
Replies: 1
Views: 1,503
Posted By stoker
Reply

Probably your bowtie has problems with reading from indexes path.
This thread may be helpful:

http://seqanswers.com/forums/showthread.php?t=3977
Forum: Bioinformatics 03-25-2011, 03:16 AM
Replies: 10
Views: 6,528
Posted By stoker
GALAXY local setup - bowtie

Dear all,
I have working local galaxy-dist on my machine and I would like to attach bowtie and tophat to it. The reference indexes setup is ok already, i can select between them in bowtie menu....
Forum: Bioinformatics 01-27-2011, 02:22 AM
Replies: 14
Views: 7,070
Posted By stoker
We have performed 2x36 paired end and obtained...

We have performed 2x36 paired end and obtained apporx 6.5 GB fastq from one lane. Unfortunately the single base qualities are low and we are trying to figure out why, together with support. I think...
Forum: Introductions 12-10-2010, 03:00 AM
Replies: 373
Views: 122,090
Posted By stoker
Hallo!

Bioinformatics PhD student from Gliwice, Poland here.
Mainly interested in RNA Seq and R programming in cancer research.

Tomasz
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