Forum: Introductions
08-26-2015, 05:16 PM
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Replies: 83
Views: 88,607
For those people following this thread.
We...
For those people following this thread.
We are recruiting Post-Doctoral Fellows for one of our large cancer genomics programs. If you are interested in working in a cutting edge research...
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Forum: Bioinformatics
03-16-2015, 10:51 PM
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Replies: 2
Views: 2,683
What version of Salmon did you use? Have you...
What version of Salmon did you use? Have you posted to the google users board for sailfish/salmon? Rob is usually very good about getting answers to questions.
I agree with you somethings seems...
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Forum: Introductions
11-25-2014, 11:09 PM
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Replies: 83
Views: 88,607
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Forum: RNA Sequencing
07-31-2014, 11:50 AM
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Replies: 12
Views: 24,985
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Forum: RNA Sequencing
07-26-2014, 09:53 PM
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Replies: 12
Views: 24,985
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Forum: Bioinformatics
02-06-2014, 10:18 PM
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Replies: 5
Views: 1,493
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Forum: RNA Sequencing
07-17-2013, 09:37 PM
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Replies: 7
Views: 4,553
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Forum: Illumina/Solexa
07-17-2013, 09:30 PM
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Replies: 9
Views: 4,130
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Forum: Sample Prep / Library Generation
06-18-2013, 01:32 PM
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Replies: 7
Views: 66,386
Great thread Phillip,
These are exactly many...
Great thread Phillip,
These are exactly many issues I've encountered in the past. My lab it actually told to set the nanodrop vertical bar at 270 to make sure the peak absorbance is not at 270. ...
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Forum: General
06-12-2013, 10:44 PM
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Replies: 33
Views: 10,768
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Forum: General
06-10-2013, 12:02 AM
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Replies: 33
Views: 10,768
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Forum: Bioinformatics
06-09-2013, 11:53 PM
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Replies: 8
Views: 7,285
Agilent adaptors are exactly the same as the...
Agilent adaptors are exactly the same as the illumina truseq less the 8bp barcode in the case of XT2 adaptors replaces the 6bp barcode in truseq. Ultimately there is little room for changes as there...
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Forum: General
06-06-2013, 11:49 PM
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Replies: 33
Views: 10,768
Didn't happen in the previous version so I'm...
Didn't happen in the previous version so I'm guessing its a result of the fix they put in for my last issue. I'm impressed with how fast they are turning around fixes so it makes it worth the effort.
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Forum: Bioinformatics
06-06-2013, 11:27 PM
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Replies: 44
Views: 32,230
We have done a decent bit of side by side...
We have done a decent bit of side by side comparisons of STAR 2.3.0 and TOPHAT 2.0.8b.
Short story is they are not very different. On most obvious counts STAR wins, faster and more unique...
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Forum: General
06-06-2013, 11:10 PM
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Replies: 33
Views: 10,768
Hi Wei,
Got a new bug during SAM->BAM...
Hi Wei,
Got a new bug during SAM->BAM conversion using samtools:
[samopen] SAM header is present: 178 sequences.
Parse error at line 580: sequence and quality are inconsistent
I pulled out...
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Forum: Bioinformatics
06-06-2013, 10:57 PM
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Replies: 5
Views: 2,614
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Forum: Bioinformatics
06-06-2013, 10:54 PM
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Replies: 5
Views: 2,614
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Forum: General
06-05-2013, 10:58 PM
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Replies: 33
Views: 10,768
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Forum: General
06-05-2013, 12:46 AM
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Replies: 33
Views: 10,768
Assuming Wei can confirm that is correct. I...
Assuming Wei can confirm that is correct. I actually understand your explanation, so thanks @sdriscoll
So if we were to set it dynamically to include read pairs within 1 standard deviation it...
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Forum: General
06-05-2013, 12:04 AM
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Replies: 33
Views: 10,768
So by --mindist does this really mean the...
So by --mindist does this really mean the sequence length that is sequenced by both read1 and read2?
I only pick on this as it was a MAJOR issue in Tophat as read lengths increased and we started...
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Forum: Sample Prep / Library Generation
06-04-2013, 09:58 PM
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Replies: 35
Views: 22,257
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Forum: RNA Sequencing
06-04-2013, 09:45 PM
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Replies: 9
Views: 15,144
We include the ERCC in most experiments now. We...
We include the ERCC in most experiments now. We see 0.2-1.5% of all reads coming from the spike-ins. Personally I see a significant amount of value in these reagents and I highly recommend them to...
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Forum: General
06-03-2013, 11:33 PM
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Replies: 33
Views: 10,768
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Forum: Bioinformatics
06-03-2013, 11:14 PM
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Replies: 4
Views: 2,168
See...
See http://www.broadinstitute.org/gatk/guide/topic?name=methods-and-workflows#Introduction
Look about half way down for lift-over
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Forum: General
06-02-2013, 12:20 AM
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Replies: 33
Views: 10,768
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