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Forum: Bioinformatics 04-29-2016, 06:58 AM
Replies: 4
Views: 1,903
Posted By ebe
Hi, in the cluster documentation, the --mem...

Hi,

in the cluster documentation, the --mem option is fixed to the memory limit of the node by default.
Anywy, I'm going to precise --mem option.
Only for information, I have precised these...
Forum: Bioinformatics 04-29-2016, 02:14 AM
Replies: 4
Views: 1,903
Posted By ebe
pbl to run hisat2 on a computer cluster with hg19

Hi,
I want to map RNAseq data (from 10 to 30 Go, single and paired-end) on complete human genome with hisat2. To do that, I use a cluster (15 nodes, 24 cores each one, 64Go RAM, workload manager...
Forum: RNA Sequencing 11-24-2015, 06:27 AM
Replies: 0
Views: 1,275
Posted By ebe
DEXseq : a known DE exon not found

Hi,

We focus on alternative splicing for one gene (with many exons).
We test several statistical methods (EdgeR, DESeq, DEXSeq) to identify DE exons, and we also calculate the PSI values with the...
Forum: Bioinformatics 09-18-2015, 06:40 AM
Replies: 1
Views: 2,774
Posted By ebe
The response from Alex Dobin, STAR's author : ...

The response from Alex Dobin, STAR's author :
using the --outFilterType Normal vs BySJout options will create slightly different SJ.out.tab counts for the following reason.
Imagine that you have a...
Forum: Bioinformatics 09-16-2015, 08:02 AM
Replies: 1
Views: 2,774
Posted By ebe
RNA-Star : SJ.out.tab differents according to 'outFilterType' value?? and

Hello,

we are using RNA-Star to our project (thank to authors!).
I don't understand a difference observed about the SJ.out.tab files (file with junctions) according to the value of...
Forum: 454 Pyrosequencing 07-02-2014, 12:52 AM
Replies: 0
Views: 1,214
Posted By ebe
overrepresented reads with a given length

Hi,

we sequence human DNA with 454 Junior, single-read. Runs are ok (number and quality of reads).
After trimming (quality>20 or 25 according to tests) and removing adapters (15nt), the reads...
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