Forum: Bioinformatics
07-24-2014, 05:44 AM
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Replies: 1
Views: 2,299
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Forum: Bioinformatics
07-24-2014, 02:15 AM
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Replies: 5
Views: 1,590
Hi luc,
In which ocasions should one use the...
Hi luc,
In which ocasions should one use the reverse complement?
I am looking at demultiplexing some data, and there are NO reads matching my barcodes. When I run FASTQC it seams like there are...
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Forum: Bioinformatics
07-24-2014, 02:01 AM
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Replies: 1
Views: 2,299
Demultiplexing 454
Dear all,
I am trying to de-multiplex a 454 fasta file.
It is a public data file. In the paper (PMID:21731642 (http://www.ncbi.nlm.nih.gov/pubmed/21731642)) the authors say that:
"The HB4a and...
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Forum: Bioinformatics
06-30-2014, 06:03 AM
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Replies: 16
Views: 14,827
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Forum: Bioinformatics
06-30-2014, 06:02 AM
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Replies: 7
Views: 7,589
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Forum: Bioinformatics
06-30-2014, 06:02 AM
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Replies: 2
Views: 12,239
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Forum: Bioinformatics
06-30-2014, 06:01 AM
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Replies: 57
Views: 41,327
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Forum: Bioinformatics
02-27-2013, 09:20 AM
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Replies: 8
Views: 4,122
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Forum: Bioinformatics
02-26-2013, 04:11 PM
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Replies: 8
Views: 4,122
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Forum: Bioinformatics
02-26-2013, 12:16 PM
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Replies: 8
Views: 4,122
Hello pmcget,
These are T47D cells, a human...
Hello pmcget,
These are T47D cells, a human breast cancer cell line, and the Transcription factor is FOXA1 ChIP-Seq.
I have checked a few peaks with the track "repeat masker", and I didn't find...
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Forum: Bioinformatics
02-26-2013, 06:32 AM
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Replies: 8
Views: 4,122
Hello pmcget,
I tried the same plot with and...
Hello pmcget,
I tried the same plot with and without replicates. The one I posted is without duplicates, which I removed using picard.
I don’t think the code has any error. I tried the same code...
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Forum: Bioinformatics
02-26-2013, 03:49 AM
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Replies: 8
Views: 4,122
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Forum: Bioinformatics
12-14-2009, 05:01 PM
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Replies: 2
Views: 1,659
Hi dawe!
Thanks for the reply! I tried with...
Hi dawe!
Thanks for the reply! I tried with your last suggestions
$comm = "qsub -S /bin/sh -l walltime=48:00:00 -o $mysh.out -e $mysh.err $mysh > $mysh.id ";
and it worked perfectly. I would...
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Forum: Bioinformatics
12-04-2009, 05:38 PM
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Replies: 2
Views: 1,659
RNA-MATE in an SGE queue manager
Hello
I am trying to use RNA-MATE in a computer cluster with an SGE queue manager. In RNA-MATE v1.1 user guide, the user is instructed to change a couple of things in the RNA-mapping.pm perl script....
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Forum: SOLiD
10-05-2009, 10:28 AM
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Replies: 35
Views: 22,722
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Forum: SOLiD
10-05-2009, 10:24 AM
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Replies: 35
Views: 22,722
Dear westerman,
Thanks for the reply
I...
Dear westerman,
Thanks for the reply
I have a collection of reads that are 35 nuc long.
In all of them there is a '.' in the same position, so when I translate from
colorspace to basesapce all...
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Forum: SOLiD
10-05-2009, 10:22 AM
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Replies: 35
Views: 22,722
Thanks for the reply
I have a collection of...
Thanks for the reply
I have a collection of reads that are 35 nuc long.
In all of them there is a '.' in the same position, so when I translate from
colorspace to basesapce all of my reads...
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Forum: SOLiD
10-05-2009, 07:54 AM
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Replies: 34
Views: 29,656
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Forum: SOLiD
10-05-2009, 07:38 AM
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Replies: 35
Views: 22,722
"N" in basespace
How come NA, NC, NT, NG all have the same colorspace code '5'.
This means that once you have N for a given base you never know what is the next base? You don't know if it is A,G,C,T ...
Right?...
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Forum: Bioinformatics
06-30-2009, 12:39 PM
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Replies: 32
Views: 36,182
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Forum: Bioinformatics
06-30-2009, 02:57 AM
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Replies: 514
Views: 223,932
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Forum: RNA Sequencing
06-24-2009, 03:30 PM
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Replies: 4
Views: 3,538
Cloonan et al
Hi n.cloonan,
And what about the files with raw data? I would like to compare my mappings with gene expression data.
(sorry about the icon, it is not the one I wanted, I thought it was a question...
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Forum: Bioinformatics
06-23-2009, 04:57 AM
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Replies: 236
Views: 617,675
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Forum: Bioinformatics
06-16-2009, 06:48 PM
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Replies: 514
Views: 223,932
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Forum: Bioinformatics
06-16-2009, 06:45 PM
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Replies: 514
Views: 223,932
Faster search for Bowtie
Hi lh3, you are right. The speed is dependent on the information it has to report.
For instance, I tried to run bowtie with the parameter -m set to 1 and it took 3hours, while previously it was...
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