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Search: Posts Made By: rboettcher
Forum: Bioinformatics 01-26-2014, 10:03 PM
Replies: 9
Views: 2,140
Posted By rboettcher
You can try to run R via sudo and see if the...

You can try to run R via sudo and see if the problems persist.
Forum: RNA Sequencing 01-17-2014, 01:48 AM
Replies: 10
Views: 2,672
Posted By rboettcher
You did not include a question or any findings in...

You did not include a question or any findings in your post, so what exactly do you want to know?
Forum: Bioinformatics 01-14-2014, 12:23 AM
Replies: 2
Views: 1,083
Posted By rboettcher
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...
Forum: Bioinformatics 01-10-2014, 05:19 AM
Replies: 4
Views: 1,208
Posted By rboettcher
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...
Forum: General 01-07-2014, 11:58 PM
Replies: 2
Views: 953
Posted By rboettcher
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...
Forum: Bioinformatics 12-04-2013, 10:57 PM
Replies: 3
Views: 1,500
Posted By rboettcher
Is this gene included in the GTF file you provide...

Is this gene included in the GTF file you provide to cufflinks? If not: did you enable the search for novel genes (--GTF-guide)?
Forum: Bioinformatics 11-27-2013, 02:49 AM
Replies: 3
Views: 2,432
Posted By rboettcher
Hi Brian, I am also interested in this...

Hi Brian,

I am also interested in this topic, so could you please keep this thread updated in case you find your answer?

Regards
Forum: Bioinformatics 11-08-2013, 01:09 AM
Replies: 7
Views: 2,841
Posted By rboettcher
I suggest to have a look a their manuscript on...

I suggest to have a look a their manuscript on arXiv where the authors made such as comparison. From my experience both tools produce similar results, see http://arxiv.org/abs/1305.3347

EDIT:...
Forum: Bioinformatics 11-07-2013, 11:47 PM
Replies: 7
Views: 2,841
Posted By rboettcher
I agree with feralBiologist, but would switch to...

I agree with feralBiologist, but would switch to featureCounts instead of HTSeq-count for performance reasons (can be run multithreaded and does not require resorted SAM file).
Forum: Bioinformatics 10-18-2013, 03:36 AM
Replies: 7
Views: 2,217
Posted By rboettcher
@bostonian I am currently struggling with...

@bostonian

I am currently struggling with the same issue, did you find a solution for your problem?
Forum: RNA Sequencing 08-30-2013, 01:58 AM
Replies: 5
Views: 2,005
Posted By rboettcher
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...
Forum: Bioinformatics 08-20-2013, 08:46 AM
Replies: 3
Views: 1,510
Posted By rboettcher
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...
Forum: Bioinformatics 08-15-2013, 02:22 AM
Replies: 1
Views: 829
Posted By rboettcher
There seems to be a related thread on SEQanswers...

There seems to be a related thread on SEQanswers already, see:

http://seqanswers.com/forums/showthread.php?t=8042
Forum: Bioinformatics 07-01-2013, 01:30 AM
Replies: 0
Views: 4,356
Posted By rboettcher
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...
Forum: Bioinformatics 06-10-2013, 12:35 AM
Replies: 46
Views: 24,536
Posted By rboettcher
Your bam/sam file needs to be name sorted for...

Your bam/sam file needs to be name sorted for HTSeq-count, see "samtools sort -n".

Regards
Forum: Bioinformatics 05-14-2013, 06:47 AM
Replies: 3
Views: 1,119
Posted By rboettcher
Scripture and Cufflinks should be on your list...

Scripture and Cufflinks should be on your list for reference-guided / mapping assembly.
Forum: Bioinformatics 05-02-2013, 03:48 AM
Replies: 3
Views: 1,269
Posted By rboettcher
There is a thread for RNA-seq tools on...

There is a thread for RNA-seq tools on SEQanswers:

http://seqanswers.com/forums/showthread.php?t=26043
Forum: Bioinformatics 05-01-2013, 04:01 AM
Replies: 10
Views: 5,200
Posted By rboettcher
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...
Forum: Bioinformatics 04-11-2013, 11:08 PM
Replies: 10
Views: 5,200
Posted By rboettcher
I experienced the same behaviour (higher p-values...

I experienced the same behaviour (higher p-values for increasing group sizes) and therefore switched to edgeR for my differential expression analysis.
You should check out the DEXSeq paper...
Forum: Bioinformatics 04-03-2013, 01:57 AM
Replies: 5
Views: 1,064
Posted By rboettcher
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...
Forum: RNA Sequencing 03-04-2013, 03:54 AM
Replies: 1
Views: 1,662
Posted By rboettcher
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...
Forum: Bioinformatics 02-05-2013, 06:45 AM
Replies: 3
Views: 739
Posted By rboettcher
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...
Forum: Bioinformatics 01-13-2013, 11:49 PM
Replies: 37
Views: 6,830
Posted By rboettcher
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...
Forum: Bioinformatics 01-09-2013, 04:27 AM
Replies: 2
Views: 774
Posted By rboettcher
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. ...
Forum: Bioinformatics 12-18-2012, 02:05 AM
Replies: 2
Views: 1,176
Posted By rboettcher
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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