Forum: Bioinformatics
09-25-2012, 08:21 PM
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Replies: 14
Views: 3,328
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Forum: Bioinformatics
09-25-2012, 05:02 PM
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Replies: 14
Views: 3,328
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Forum: Bioinformatics
09-19-2012, 12:29 PM
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Replies: 1
Views: 1,664
Yes, you are right. Tophat tries to align the...
Yes, you are right. Tophat tries to align the whole reads first and then the unmapped reads are split into small segments so in your case 9 (--segment-length 20) they would be split into 20bp...
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Forum: Bioinformatics
09-13-2012, 06:17 AM
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Replies: 56
Views: 12,945
Alright... So I ran the new PathSeq_BWA version...
Alright... So I ran the new PathSeq_BWA version and here are the results. I had ~65 million filtered reads and it took ~8 hours to finish and produced 177308 unmapped reads. This was run on 19 nodes...
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Forum: Bioinformatics
09-12-2012, 12:52 PM
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Replies: 56
Views: 12,945
Looks like there is a bug in...
Looks like there is a bug in Preprocessed_Reads.com file. Line 18 says exit and the script quits.
After commenting the line, the script runs fine.
@ n_para=$#
# Reading environmental...
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Forum: Bioinformatics
09-12-2012, 07:31 AM
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Replies: 56
Views: 12,945
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Forum: Introductions
08-30-2012, 02:10 PM
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Replies: 4
Views: 1,574
Hi and welcome to SEQanswers.
Newbler is an...
Hi and welcome to SEQanswers.
Newbler is an commercial software and you would need a license to install it. Maybe you want to look at open source software for de novo assembly...
Here is a list:...
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Forum: Bioinformatics
08-30-2012, 08:59 AM
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Replies: 56
Views: 12,945
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Forum: Bioinformatics
04-17-2012, 01:00 PM
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Replies: 25
Views: 13,235
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Forum: Bioinformatics
04-16-2012, 07:37 AM
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Replies: 1
Views: 4,480
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Forum: Bioinformatics
04-16-2012, 07:28 AM
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Replies: 25
Views: 13,235
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Forum: Bioinformatics
03-01-2012, 09:26 AM
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Replies: 10
Views: 6,013
Hi Cole,
I see something similar with my data...
Hi Cole,
I see something similar with my data too. cuffdiff produces very few significant (Significant: Yes) genes although I have not compared with other methods. I am using cufflinks v1.3.0 but...
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Forum: Bioinformatics
02-13-2012, 07:09 PM
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Replies: 10
Views: 4,364
Hi Diya,
Can you please post the command that...
Hi Diya,
Can you please post the command that you are using to run Tophat. Also, the Tophat version you are using is 1.2.0 which is more than an year old and there have been lots of changes since...
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Forum: Bioinformatics
01-20-2012, 11:55 AM
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Replies: 12
Views: 3,930
That is wrong. cuffdiff can be used to compute...
That is wrong. cuffdiff can be used to compute the differential expression between two conditions. For two conditions, you need to give the sample names as comma separated values and differentiate...
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Forum: Bioinformatics
12-28-2011, 01:23 PM
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Replies: 6
Views: 12,188
For annotating the VCF file you can use the...
For annotating the VCF file you can use the Ensembl Variant Effect Predictor. It is very helpful and can also produce SIFT, PolyPhen and Condel consensus.
http://ensembl.org/tools.html
I would...
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Forum: Site Feedback/Suggestions
12-02-2011, 11:10 AM
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Replies: 7
Views: 17,283
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Forum: Site Feedback/Suggestions
11-27-2011, 11:14 AM
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Replies: 7
Views: 17,283
Support for Tapatalk?
Hi,
It would be great if SEQanswers has Tapatalk support. With many users now having smart phones and tablets, it would be easy to keep track of the threads and replies on the go using the Tapatalk...
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Forum: Introductions
11-27-2011, 12:24 AM
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Replies: 83
Views: 88,579
Thank You, Jon for fixing the bug and for the...
Thank You, Jon for fixing the bug and for the cufflinks_exclude files. :)
I was about to post about HiSeq data and Illumina's switch to Sanger quality scores (as I had to update your script to...
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Forum: Introductions
11-26-2011, 09:28 PM
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Replies: 83
Views: 88,579
I believe line #316 in the...
I believe line #316 in the RNAseq_MensFormal_Mac.sh should be as below. Or else no matter what user response you give (Yes/No), the tophat tag will always be set to TophatPE_GTF.
# TOPHAT_TAG...
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Forum: Literature Watch
11-24-2011, 03:58 AM
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Replies: 46
Views: 42,069
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Forum: Literature Watch
11-24-2011, 03:38 AM
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Replies: 46
Views: 42,069
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Forum: Introductions
11-20-2011, 05:33 PM
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Replies: 83
Views: 88,579
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Forum: Bioinformatics
11-17-2011, 03:20 PM
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Replies: 1
Views: 3,395
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Forum: Bioinformatics
08-02-2011, 01:38 PM
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Replies: 6
Views: 5,513
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Forum: Literature Watch
07-27-2011, 03:07 PM
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Replies: 46
Views: 42,069
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