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Search: Posts Made By: marb
Forum: Bioinformatics 12-13-2011, 03:56 AM
Replies: 4
Views: 2,262
Posted By marb
I've tested cufflinks processing on other data...

I've tested cufflinks processing on other data and then cufflinks recognised them correctly as 57bp x 57bp.
Hence I know that there is the mistake at tophat processing fastq files level.

I know...
Forum: Bioinformatics 12-12-2011, 01:32 AM
Replies: 4
Views: 2,262
Posted By marb
Do you think about header of bam file? I...

Do you think about header of bam file?
I obtained 28 fastq files from Casava - 14 right-end (R1) 14 left-end (R2).
I have processed them by tophat.
Forum: Bioinformatics 12-11-2011, 09:26 AM
Replies: 4
Views: 2,262
Posted By marb
Cufflinks doesn't recognize read type

Hello.
I used Cufflinks to process data from tophat.
My data come from Illumina and are pair-end type.

I type following command:
/path/cufflinks tophat_out/accepted_hits.bam -o cuff_out

...
Forum: Bioinformatics 12-06-2011, 05:26 AM
Replies: 2
Views: 1,087
Posted By marb
Thank you for your sugestion. In the past I...

Thank you for your sugestion.
In the past I even used the screen but I forget about it.
Greeting.
Forum: Bioinformatics 12-06-2011, 04:46 AM
Replies: 2
Views: 1,087
Posted By marb
Cufflinks and nohup?

Is it possible to run cufflinks in background with nohup?

When I tried run is as below it didn't work :(

nohup path_to_cufflinks/cufflinks accepted_hits.bam &

Nohup file was created but it...
Forum: Bioinformatics 12-03-2011, 01:27 AM
Replies: 3
Views: 2,540
Posted By marb
In my opinion your solution is very good. It's...

In my opinion your solution is very good. It's works!!!
Thank you very much for help.
Forum: Bioinformatics 12-02-2011, 12:38 PM
Replies: 3
Views: 2,540
Posted By marb
Tophat - processing several files fastq

Hello.
I use data from Illumina GA IIx procesed by Casava to fastq files.
There is several fastq files in each lane.
How to processing that all files at same time by tophat?
I tried type: but...
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