Forum: Bioinformatics
04-08-2013, 07:49 AM
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Replies: 0
Views: 2,291
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Forum: RNA Sequencing
03-26-2013, 01:54 PM
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Replies: 0
Views: 1,713
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Forum: Bioinformatics
03-07-2013, 12:46 PM
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Replies: 313
Views: 124,310
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Forum: Bioinformatics
01-03-2013, 03:00 PM
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Replies: 6
Views: 4,796
Any progress?
Has anyone figured this out? I'm struggling as well. In ggplot2, it seems like the issue is an inability to change the "default" layer of the plot, on account of the "data" being fed from the method,...
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Forum: Bioinformatics
07-14-2010, 02:49 PM
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Replies: 5
Views: 5,731
I'm experiencing the same issue. I'm using...
I'm experiencing the same issue. I'm using cufflinks 0.8.3 (the 7/2 release) and the -c option doesn't seem to work as described in the manual. As extreme examples, I have loci that are "OK" for...
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Forum: Bioinformatics
07-13-2010, 08:04 AM
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Replies: 10
Views: 3,478
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Forum: Bioinformatics
07-02-2010, 08:10 AM
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Replies: 10
Views: 3,478
Cuffcompare Xlocus error
Hi all -
I've been struggling with a strange error in CuffCompare.
I'm using the new cufflinks package (0.8.3) for 4 samples mapped using Tophat. After generating Cufflinks GTFs for each...
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Forum: Bioinformatics
12-29-2009, 08:48 PM
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Replies: 34
Views: 18,254
Cufflinks outputs duplicate GTF entries?
Hi all-
First off, thank you Cole for Cufflinks. It will be very useful for the type of RPKM analysis I'd like to.
I'm having a bit of trouble with the GTF output files when I plug them into...
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Forum: Illumina/Solexa
08-24-2009, 04:41 PM
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Replies: 18
Views: 6,982
Though I also think PCR bias is likely the...
Though I also think PCR bias is likely the primary culprit here, you might also consider problems caused during read mapping. Depending on which mapping/alignment algorithm you are using (and the...
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Forum: Bioinformatics
08-05-2009, 06:10 PM
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Replies: 6
Views: 2,956
Tophat does a really nice job mapping splice...
Tophat does a really nice job mapping splice junctions without a set of known splice sites. It works very well with short Solexa reads, though I presume it requires a certain degree of read depth.
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Forum: Bioinformatics
08-04-2009, 03:36 PM
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Replies: 22
Views: 9,740
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Forum: Bioinformatics
08-04-2009, 03:01 PM
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Replies: 22
Views: 9,740
Thanks Cole.
Sorry for the sequential...
Thanks Cole.
Sorry for the sequential posting, but...Taking a closer look, it looks like the issue could be the base qualities returned in the 'accepted_hits.sam' output from Tophat.
I'm using...
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Forum: Bioinformatics
08-04-2009, 02:28 PM
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Replies: 22
Views: 9,740
Is there any way to have Tophat output an...
Is there any way to have Tophat output an appropriate value for the "Mapping Qualities" field in the SAM format? At present, it outputs a straight "255" (which the SAM specification suggests when...
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Forum: Bioinformatics
08-04-2009, 09:39 AM
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Replies: 292
Views: 172,196
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Forum: Bioinformatics
08-03-2009, 08:21 AM
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Replies: 22
Views: 9,740
Tophat 1.0.10
Hi Cole-
The new version (1.0.10) seems to be working fine for me. Strand orientation in the output SAM file looks good, as far as I can tell.
Thanks so much for the rapid turnaround!
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Forum: Bioinformatics
07-30-2009, 05:28 PM
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Replies: 3
Views: 5,807
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Forum: Bioinformatics
07-30-2009, 05:27 PM
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Replies: 22
Views: 9,740
Read orientation in Tophat SAM output
Though I've been successful in getting Tophat's SAM output into a SAMtools pileup, I've been having considerable trouble with a related issue.
According to the SAM specifications, for each...
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Forum: Bioinformatics
07-23-2009, 07:42 AM
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Replies: 3
Views: 5,807
Interpretation of columns in MAQ SNP output?
Hi all-
Apologies if this information has been posted elsewhere - I wasn't able to find what I was looking for searching the forums.
I'm using MAQ cns2SNP (and SNPfilter) to call SNPs on short...
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Forum: RNA Sequencing
04-30-2009, 12:11 PM
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Replies: 25
Views: 14,032
Hey Ali-
Just wanted to say thanks for your...
Hey Ali-
Just wanted to say thanks for your help. Reducing the cache size seemed to help get through the analysis without memory errors, despite taking a bit longer.
I've got some additional...
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Forum: RNA Sequencing
04-24-2009, 11:28 AM
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Replies: 25
Views: 14,032
Thanks Ali -
I'm running ERANGE locally on a...
Thanks Ali -
I'm running ERANGE locally on a MacBook Pro with 4gb RAM, and not running ANYTHING else during the analysis. I've got the cache set to 2000000 for the RDS file.
This has been more...
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Forum: RNA Sequencing
04-24-2009, 09:24 AM
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Replies: 25
Views: 14,032
ERANGE error message
Hi all-
I've used successfully used ERANGE3.0.1 in the past for some RNA-seq analysis. I'm now running into some problems getting through the RunStandardAnalysis script.
My reads are...
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Forum: RNA Sequencing
02-20-2009, 03:49 PM
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Replies: 25
Views: 14,032
Also struggling with ERANGE...
Not sure if this thread is still going, but i'll give it a shot.
I'm also trying to get ERANGE (v2.1) off the ground and having some major problems.
I'm running through the shell on Mac OS X...
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Forum: Bioinformatics
02-20-2009, 07:51 AM
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Replies: 99
Views: 47,747
Mapview overflow error
@baohua100
Thanks for all of your work on MapView...it's been very helpful so far and for the most part, working well.
I am having one problem that's given me some trouble. I'm using MapView...
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