Forum: Bioinformatics
05-20-2015, 01:24 AM
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Replies: 2
Views: 2,297
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Forum: Bioinformatics
01-13-2015, 06:08 AM
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Replies: 8
Views: 3,608
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Forum: Bioinformatics
06-23-2014, 03:02 AM
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Replies: 1
Views: 3,043
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Forum: Bioinformatics
06-23-2014, 12:36 AM
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Replies: 1
Views: 3,043
Velvet assembler ambiguous calls
Hello,
I'm using Velvet assembler and I've a little doubt.
After reading Velvet documentation I know that one gap in output assembly is represented by minimum of 10 N's. And that the number of...
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Forum: Ion Torrent
06-09-2014, 01:32 AM
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Replies: 14
Views: 16,109
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Forum: Ion Torrent
03-25-2014, 07:01 AM
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Replies: 14
Views: 16,109
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Forum: Ion Torrent
03-25-2014, 05:07 AM
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Replies: 14
Views: 16,109
Variant Calling outside Torrent Suite and TVC
Hello,
After trying to build Torrent Suite 4 for weeks on a RedHat Linux without success (I got compiled programs but not working with my Linux Architecture), and exploring all the tools they...
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Forum: Bioinformatics
11-18-2013, 02:35 AM
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Replies: 5
Views: 3,080
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Forum: Bioinformatics
11-17-2013, 11:54 PM
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Replies: 5
Views: 3,080
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Forum: Bioinformatics
11-15-2013, 06:34 AM
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Replies: 5
Views: 3,080
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Forum: Bioinformatics
11-06-2013, 03:12 AM
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Replies: 3
Views: 1,955
Then I guess 1000genomes reference for phase 2...
Then I guess 1000genomes reference for phase 2 is:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz
Maybe I miss explained myself. I...
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Forum: Bioinformatics
11-06-2013, 12:53 AM
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Replies: 3
Views: 1,955
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Forum: Bioinformatics
11-05-2013, 07:34 AM
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Replies: 3
Views: 1,955
1000 genomes human reference
Hello,
I'm using hg19.
As you may know when you perform variant calling, reference variation allele may be biased due to the human reference we use (it's very uncommon but it does happen).
I...
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Forum: Bioinformatics
10-04-2013, 12:32 AM
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Replies: 0
Views: 2,041
Nextera Expanded Exome BWA aln
Hello,
I'm trying to align Nextera Expanded Exome (62Mb) samples from HiSeq 2000 (Paired end ~99bp insert size) with BWA aln.
I'm having some troubles. Calculate SA coordinate seems to take a...
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Forum: Bioinformatics
09-30-2013, 07:14 AM
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Replies: 3
Views: 4,624
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Forum: Bioinformatics
09-30-2013, 03:52 AM
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Replies: 3
Views: 4,624
BED to RefSeq gene format
Hello,
I would like to convert a BED interval file to RefSeq format. I need this to use it among with GATK DepthOfCoverage.
I've been trying loading custom track on UCSC....
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Forum: Bioinformatics
09-25-2013, 08:53 AM
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Replies: 6
Views: 3,982
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Forum: Bioinformatics
09-24-2013, 11:54 PM
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Replies: 6
Views: 3,982
Merging two bacteria de novo assemblies into one
Hello,
I'm trying to merge a bacterial genome assembly done by myself with Velvet with another I got from partner.
Both assemblies data come from Illumina MiSeq platform (Paired End).
I've a...
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Forum: Bioinformatics
09-24-2013, 12:54 AM
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Replies: 2
Views: 3,290
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Forum: Bioinformatics
09-20-2013, 01:31 AM
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Replies: 2
Views: 3,290
CISA assembly contig integrator error
Hello,
I'm trying to use CISA to merge and optimize two de novo bacterial assemblies.
Process seems to work fine until the very last step. I'm getting this error:
Traceback (most recent call...
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Forum: Bioinformatics
09-13-2013, 07:59 AM
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Replies: 7
Views: 6,514
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Forum: Bioinformatics
09-13-2013, 07:23 AM
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Replies: 6
Views: 11,684
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Forum: Bioinformatics
07-22-2013, 02:42 AM
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Replies: 6
Views: 9,681
Hello Heisman,
I'm trying sed command with...
Hello Heisman,
I'm trying sed command with no success:
sed -e 's,chrX,chr23,' -e 's,chrY,chr24' input.bed
sed: -e expression #2, char 12: unterminated `s' command
Fixed missing a comma...
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Forum: Bioinformatics
07-19-2013, 06:17 AM
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Replies: 6
Views: 9,681
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Forum: Bioinformatics
07-19-2013, 05:57 AM
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Replies: 6
Views: 9,681
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