Forum: Bioinformatics
01-26-2014, 10:03 PM
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Replies: 9
Views: 3,134
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Forum: RNA Sequencing
01-17-2014, 01:48 AM
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Replies: 10
Views: 4,387
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Forum: Bioinformatics
01-14-2014, 12:23 AM
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Replies: 2
Views: 1,960
Try bedtools intersect with your Cufflinks GTF...
Try bedtools intersect with your Cufflinks GTF and the GTF you used as reference annotation to see if there is any known annotation in the regions identified by Cufflinks (which should not be the...
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Forum: Bioinformatics
01-10-2014, 05:19 AM
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Replies: 4
Views: 1,947
Novel depends on which reference annotation you...
Novel depends on which reference annotation you are using. If there is more than one source, start with filtering out everything that shows any overlap with any known gene. Next, you can filter for...
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Forum: General
01-07-2014, 11:58 PM
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Replies: 2
Views: 1,443
Hi lre1234,
If you are looking at a pool of...
Hi lre1234,
If you are looking at a pool of samples this might actually be a true thing, but I would check for repetitive or very similar sequences on the other side of the fusion to check if you...
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Forum: Bioinformatics
12-04-2013, 10:57 PM
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Replies: 3
Views: 3,071
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Forum: Bioinformatics
11-27-2013, 02:49 AM
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Replies: 3
Views: 3,700
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Forum: Bioinformatics
11-08-2013, 01:09 AM
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Replies: 7
Views: 4,144
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Forum: Bioinformatics
11-07-2013, 11:47 PM
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Replies: 7
Views: 4,144
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Forum: Bioinformatics
10-18-2013, 03:36 AM
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Replies: 7
Views: 3,344
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Forum: RNA Sequencing
08-30-2013, 01:58 AM
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Replies: 5
Views: 2,945
Hi Alex,
just to be sure: did you use...
Hi Alex,
just to be sure: did you use Cufflink's FPKM for DESeq?
(a) Did you check the quality of these reads? Did both conditions give equal output (number of reads, quality)?
(b) You can...
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Forum: Bioinformatics
08-20-2013, 08:46 AM
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Replies: 3
Views: 2,477
I don't think this is a problem of the heatmap...
I don't think this is a problem of the heatmap function, but more of your system. It seems that your data matrix is quite huge, so may I ask on what kind of hardware you are creating this heatmap? It...
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Forum: Bioinformatics
08-15-2013, 02:22 AM
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Replies: 1
Views: 1,483
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Forum: Bioinformatics
07-01-2013, 01:30 AM
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Replies: 0
Views: 5,043
Public gene prediction GTFs for human
Hi all,
I am currently searching for publicly available gene predictions (by programs such as GENSCAN) for human that are in GTF format. I figured that various programs should have been run on...
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Forum: Bioinformatics
06-10-2013, 12:35 AM
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Replies: 46
Views: 33,850
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Forum: Bioinformatics
05-14-2013, 06:47 AM
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Replies: 3
Views: 2,012
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Forum: Bioinformatics
05-02-2013, 03:48 AM
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Replies: 3
Views: 1,987
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Forum: Bioinformatics
05-01-2013, 04:01 AM
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Replies: 10
Views: 8,029
I just saw that Trapnell et al. released a new...
I just saw that Trapnell et al. released a new Cufflinks/Cuffdiff version (2.1 http://cufflinks.cbcb.umd.edu/index.html) and address exactly the issues we discussed here in their description. I have...
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Forum: Bioinformatics
04-11-2013, 11:08 PM
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Replies: 10
Views: 8,029
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Forum: Bioinformatics
04-03-2013, 01:57 AM
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Replies: 5
Views: 2,092
Hi Amative,
what kind of reference did you...
Hi Amative,
what kind of reference did you provide? Bowtie2 is not splicing aware, so it is not able to deal with reads spanning splice junctions. Therefore, it can only be used to align against...
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Forum: RNA Sequencing
03-04-2013, 03:54 AM
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Replies: 1
Views: 2,320
Cuffdiff is known to be very stringent,...
Cuffdiff is known to be very stringent, especially if the variance within your groups is quite high. If you are accustomed to R, then you can try to use methods such as DESeq or edgeR for...
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Forum: Bioinformatics
02-05-2013, 06:45 AM
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Replies: 3
Views: 1,651
Hi HSV-1,
You can use bowtie with option -c...
Hi HSV-1,
You can use bowtie with option -c TCGTGACGGTA
and specify that you want to output all alignments via option -a.
However, in this case you also need to specify that only perfect matches...
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Forum: Bioinformatics
01-13-2013, 11:49 PM
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Replies: 37
Views: 9,127
Since the U.S. are the only state in the world...
Since the U.S. are the only state in the world funding research and none of the big U.S. companies have benefits from scientific results produced in other countries... (please note the irony).
If...
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Forum: Bioinformatics
01-09-2013, 04:27 AM
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Replies: 2
Views: 1,365
Hello jparsons,
I used cufflinks and...
Hello jparsons,
I used cufflinks and cuffdiff with GSNAP alignments and it worked fine, so you do not need to stick to TopHat necessarily as long as the sam/bam-files have all required columns. ...
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Forum: Bioinformatics
12-18-2012, 02:05 AM
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Replies: 2
Views: 1,882
TopHat2 is designed for RNAseq and therefore...
TopHat2 is designed for RNAseq and therefore splicing aware, whereas bowtie2 is designed for DNAseq and therefore cannot handle splice junctions.
Since your RNAseq is expected to come from exons...
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