Forum: Industry Jobs!
06-30-2014, 04:58 PM
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Replies: 0
Views: 3,719
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Forum: Open Genomics Engine Project
05-23-2014, 07:29 AM
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Replies: 1
Views: 31,960
BioDT-Lab. public resource for bioinformaticians
Sorry for repost. Looks like this announcement well fit to this topic
BioDatomics has launched its BioDT Labs program, which offers free,
cloud-based access for qualified bioinformaticians to...
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Forum: Bioinformatics
05-23-2014, 07:24 AM
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Replies: 1
Views: 2,164
Tutorials for a platform
Hi Everyone,
Update: we are planning to create a series of tutorials for our platform. Here is a first one: https://www.youtube.com/watch?v=9xsL-OjoitI
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Forum: Bioinformatics
05-14-2014, 03:19 PM
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Replies: 1
Views: 2,164
BioDT-Lab. public resource for bioinformaticians
BioDatomics has launched its BioDT Labs program, which offers free,
cloud-based access for qualified bioinformaticians to BioDatomics'
Hadoop-powered bioanalytics platform. BioDT Labs differs...
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Forum: RNA Sequencing
11-22-2012, 05:16 AM
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Replies: 16
Views: 5,521
solution
The help is here:
read #1 (HWI-ST993:228:C0RWJACXX:6:2316:17166:97507) does not have a matching mate in the same order (HWI-ST993:228:C0RWJACXX:6:2316:12084:97378 found instead)
The Red text...
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Forum: Bioinformatics
07-05-2012, 08:17 PM
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Replies: 147
Views: 59,664
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Forum: RNA Sequencing
06-11-2012, 07:29 AM
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Replies: 16
Views: 5,521
temproary solution
you can try to rename
WIGTC-HISEQ:4:1101:1155:2046#ACAGTG/2;0 to WIGTC-HISEQ:4:1101:1155:2046#ACAGTG/1;0 in the paired file.
I mean make replacement for all read names in the second file to have...
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Forum: Bioinformatics
06-11-2012, 06:28 AM
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Replies: 147
Views: 59,664
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Forum: Bioinformatics
04-30-2012, 06:01 PM
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Replies: 13
Views: 10,561
Error:
+1 to all of you:
I run this command:
$TOPHAT -o $DEST -C -Q --bowtie1 -p 60 -r 200 --mate-std-dev 30 --report-secondary-alignments --report-discordant-pair-alignments --coverage-search...
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Forum: Bioinformatics
03-17-2012, 02:53 PM
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Replies: 32
Views: 16,460
Pindel to Dindel
I made improved version of script.
I have a several questions to someone who know how dindel work:
1. Can we replace INV on DEL+INS?
2. Can we do the same for RPL and TD?
3. Do we need to...
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Forum: Bioinformatics
03-17-2012, 11:51 AM
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Replies: 32
Views: 16,460
convert from pindel vcf to dindel format
I ended up with following script:
cat XXXX_D.vcf | grep DEL | awk '{print $1,"\t",$2,"\t&&&"$4}'| sed -e 's/&&&./-/'> XXXX_D.dindel.del
cat XXXX_SI.vcf | grep INS | awk '{print...
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Forum: Bioinformatics
03-15-2012, 07:05 PM
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Replies: 147
Views: 59,664
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Forum: Bioinformatics
03-13-2012, 01:22 PM
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Replies: 147
Views: 59,664
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Forum: Bioinformatics
03-12-2012, 05:34 PM
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Replies: 147
Views: 59,664
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Forum: Bioinformatics
03-10-2012, 01:03 PM
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Replies: 147
Views: 59,664
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Forum: Bioinformatics
03-10-2012, 12:32 PM
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Replies: 147
Views: 59,664
Hi KaiYe,
I have an error message during...
Hi KaiYe,
I have an error message during run pindel2vcf.
The executing command was:
pindel2vcf -r $REFGENOME -R hg19b37 -d 20120310 -p 5173N_TD.res -v 5173N_TD.res2.vcf
The last few lines...
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Forum: Bioinformatics
03-02-2012, 08:48 AM
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Replies: 147
Views: 59,664
It was a quick reply!!! Thanks.
I have a...
It was a quick reply!!! Thanks.
I have a several more questions now.
1. Does it mean that Pindel does not check flag that this read is duplicate?
2. If you have count it independently maybe it...
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Forum: Bioinformatics
03-02-2012, 07:15 AM
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Replies: 147
Views: 59,664
Hi KaiYe,
I used MarkDuplicates from Picard...
Hi KaiYe,
I used MarkDuplicates from Picard and mark duplicates but did not removed them.
I have a question does pindel need file with removed duplicates or can work with Marked ones?
Thank...
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