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Forum: Bioinformatics 02-26-2015, 01:21 AM
Replies: 25
Views: 21,334
Posted By pascal
I my case I hade to add "-lpthread" to the make...

I my case I hade to add "-lpthread" to the make file:

ROOTLIBS = -L$(ROOTSYS)/lib -ldl -lpthread -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d \
-lGpad -lTree -lRint -lMatrix...
Forum: Bioinformatics 05-19-2014, 06:43 AM
Replies: 2
Views: 2,523
Posted By pascal
Install the csh bash. In Ubuntu you can do that...

Install the csh bash. In Ubuntu you can do that by:

sudo apt-get install csh

Afterwards it worked for me (only single core though).
Forum: RNA Sequencing 10-19-2011, 10:59 AM
Replies: 21
Views: 5,515
Posted By pascal
Sorry, I have stopped working on this data set....

Sorry, I have stopped working on this data set. If I continue I will let you know.
Forum: Bioinformatics 07-24-2011, 03:14 AM
Replies: 11
Views: 7,930
Posted By pascal
For me it turned out, that this error message...

For me it turned out, that this error message probably occurred due to insufficient memory. I ran the same job on a cluster without any problems. Cuffdiff used over 32GB of ram + some swap.
Forum: Bioinformatics 07-10-2011, 02:37 AM
Replies: 11
Views: 7,930
Posted By pascal
I compiled cuffdiff from source and still get...

I compiled cuffdiff from source and still get this error:

terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

I am using cufflinks 1.0.3 on Ubuntu 10.10,...
Forum: Bioinformatics 04-11-2011, 03:03 AM
Replies: 10
Views: 2,931
Posted By pascal
Same here. It seems like, it depends on the order...

Same here. It seems like, it depends on the order of the samples. When I run



Cuffcompare reports this error



When I leave out the erroneous sample 10, no error occurs. BUT, and this is...
Forum: RNA Sequencing 06-04-2010, 02:22 AM
Replies: 21
Views: 5,515
Posted By pascal
Hi, I splitted the fastq files with fastx...

Hi,

I splitted the fastq files with fastx into the original paired end files (positions 1-75 and 77-151) and ran TopHat with default settings. In the paper they did use:



So the difference...
Forum: RNA Sequencing 05-26-2010, 06:36 AM
Replies: 21
Views: 5,515
Posted By pascal
syslm01, have you received an answer from SRA? I...

syslm01, have you received an answer from SRA? I want to analyze the same dataset...
Forum: RNA Sequencing 05-11-2010, 10:58 AM
Replies: 3
Views: 2,975
Posted By pascal
You might wanna take a look at this publication:...

You might wanna take a look at this publication:

Ramsköld,D. et al. (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS computational biology,...
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