[galaxy-user] cufflinks analysis using .bam files generated by LifeScope (ABI 5500 Sequencer)

2012-12-13 Thread Davide Degli Esposti
and then apply TopHat? I thank you very much for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France

[galaxy-user] Building a combined annotated transcriptome to use as a reference annotation in RNA-Seq analysis

2013-01-03 Thread Davide Degli Esposti
transcriptomes of the UCSC known genes, Ensembl and Vega. My question is how do you build such a combined file? For the moment, I was able just to compare my data with an annotated transcriptome obtained only by UCSC. I thank you for your help Best regards Davide Degli Esposti --- Davide Degli Esposti

[galaxy-user] reference annotation for whole transcriptome RNA-Seq

2013-01-29 Thread Davide Degli Esposti
Dear all, I am trying to get an exhaustive reference annotation for RNA-Seq analysis. I was thinking that the patched GTF annotation files for cufflinks Jeremy indicates in RNA-Seq step by step tutorial should be fine for me, but I am not able to find on the Shared data Data libraries. Have

[galaxy-user] running time of Cufflinks on main Galaxy

2013-01-31 Thread Davide Degli Esposti
or are the servers currently overused? Thank you for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France

[galaxy-user] error running cufflinks

2013-02-01 Thread Davide Degli Esposti
Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France --- This message and its attachments are strictly

[galaxy-user] error message running Cufflinks on local galaxy

2013-02-01 Thread Davide Degli Esposti
0.05 -j 0.15 -p 4 -G /Users/davidedegliesposti/galaxy-dist/database/files/000/dataset_2.dat -N Error running cufflinks. return code = 127 /bin/sh: cufflinks: command May this be due to an error of installation? Thank you for your help Davide --- Davide Degli Esposti, PhD Epigenetic (EGE

[galaxy-user] min alignement count

2013-04-12 Thread Davide Degli Esposti
or if the counts are 10 for at least one sample the test is performed? I thank you for your help Best regards davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08