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Search: Posts Made By: Uwe Appelt
Forum: Bioinformatics 09-16-2010, 12:46 AM
Replies: 9
Views: 9,440
Posted By Uwe Appelt
I also receive this error message with TopHat...

I also receive this error message with TopHat 1.0.14. I, however, get it for the first time and my read-config is somewhat unusual, because i have "very few" reads that poorly align to the reference...
Forum: Bioinformatics 09-15-2010, 10:35 AM
Replies: 7
Views: 3,312
Posted By Uwe Appelt
@mendl7: accepted_hits.sam indeed does...

@mendl7:

accepted_hits.sam indeed does contain split-read-alignments. At least for me, but i might miss your point. Does the following deliver want you're looking for?

fgrep --invert-match...
Forum: Bioinformatics 09-15-2010, 05:07 AM
Replies: 5
Views: 9,331
Posted By Uwe Appelt
Hi Simon, thank you so much for that chunk...

Hi Simon,

thank you so much for that chunk of code, it works like a charme! I worked out a solution of my own as well, but besides the obvious (e.g. poor parsing) drawbacks, fgrep appears to...
Forum: Bioinformatics 09-14-2010, 08:13 AM
Replies: 5
Views: 9,331
Posted By Uwe Appelt
Extract unaligned reads (Tophat) from FastQ

I would like to further examine reads that Tophat didn't manage to align in a first run and i wonder, if there is any easy way to get these reads. With Bowtie this would be easy using the "--un"...
Forum: Bioinformatics 09-14-2010, 07:26 AM
Replies: 4
Views: 3,597
Posted By Uwe Appelt
I also thought doing such thresholding should be...

I also thought doing such thresholding should be a considerable idea. For me it turned out, it's not. Because applying any more or less arbitrary thresholds to FPKM values is 1st difficult to explain...
Forum: Bioinformatics 09-14-2010, 12:51 AM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
I btw started to remove the duplicate entries...

I btw started to remove the duplicate entries manually, which can be done quickly unless there are not too many of them. And it appears there are very few duplicates - i managed to correct four...
Forum: Bioinformatics 09-09-2010, 12:44 AM
Replies: 10
Views: 2,660
Posted By Uwe Appelt
Hi tsucheta, i'm not really sure, what you...

Hi tsucheta,

i'm not really sure, what you fed into Tophat?! Fastq, but what code? Tophat will not work with color-spaced reads, i mentioned that. So i assume, you scriptually translated into...
Forum: Bioinformatics 09-06-2010, 01:22 AM
Replies: 10
Views: 2,660
Posted By Uwe Appelt
Hi tsucheta, you're right, Tophat isn't able...

Hi tsucheta,

you're right, Tophat isn't able to handle color-space reads, so you definitely have to stick with bowtie, which shouldn't be a problem at all, unless your reads are not sequenced too...
Forum: Bioinformatics 09-06-2010, 01:05 AM
Replies: 1
Views: 2,445
Posted By Uwe Appelt
Hi fugenli, although your setup appears a...

Hi fugenli,

although your setup appears a little different, the "duplicate gff id" issue has been discussed in detail here (http://seqanswers.com/forums/showthread.php?t=3493) (start reading from...
Forum: Bioinformatics 09-06-2010, 12:54 AM
Replies: 1
Views: 2,809
Posted By Uwe Appelt
Hi liuxq, this is not a mouse-specific...

Hi liuxq,

this is not a mouse-specific problem and has been discussed in detail here (http://seqanswers.com/forums/showthread.php?t=3493) (start reading from post #7). Unfortunately no fix has...
Forum: Bioinformatics 09-01-2010, 05:34 AM
Replies: 7
Views: 3,964
Posted By Uwe Appelt
Tophat Bug in Paired-End Mode? (reproducable)

I've just tried to reproduce the tophat behavior described in post #1 and tophat indeed appears to report buggy alignments in this particular case:

sa_1.txt:
@HWUSI-EAS697:1:73:6760:7084#0/1...
Forum: Bioinformatics 09-01-2010, 04:25 AM
Replies: 7
Views: 3,964
Posted By Uwe Appelt
I tend to disagree. Assuming the initially...

I tend to disagree. Assuming the initially provided SAM output is complete, we definitely have a bug here, because -as i mentioned- we cannot deny, what the SAM-flags are telling! And they indicate,...
Forum: Bioinformatics 09-01-2010, 02:52 AM
Replies: 7
Views: 3,964
Posted By Uwe Appelt
In this case, i wouldn't mess up any alignment...

In this case, i wouldn't mess up any alignment settings, because it would mean that there is indeed a serious problem! Assuming that the SAM-flags (147 and 99 as provided in post #1) indicate a...
Forum: Bioinformatics 08-31-2010, 10:36 AM
Replies: 7
Views: 3,964
Posted By Uwe Appelt
Hi Santa ;-) blating the reads provided...

Hi Santa ;-)

blating the reads provided above against HG19 indeed returns some more alignments that are at least close to optimal and thus maybe considered by tophat (didn't looked at the...
Forum: Bioinformatics 08-16-2010, 04:30 AM
Replies: 5
Views: 6,599
Posted By Uwe Appelt
Hi Memo, this actually does appear logical...

Hi Memo,

this actually does appear logical to me, because Cole described in his paper (http://dx.doi.org/10.1038/nbt.1621, see online-Methods, section "Analysis of gene expression and regulation...
Forum: Bioinformatics 08-16-2010, 03:55 AM
Replies: 2
Views: 2,495
Posted By Uwe Appelt
This is most likely due to the status of the...

This is most likely due to the status of the v0.8.4 (svn r1370, 16-Jul-2010). Cole has provided this snapshot prerelease to overcome the "duplicate gff id" errors introduced in v0.8.3 (discussed in...
Forum: Bioinformatics 07-30-2010, 12:53 AM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
Not sure, why you think your experiences to be...

Not sure, why you think your experiences to be the opposite of what others desribe - it's exactly what the latest posts are about, isn't it.
Forum: Bioinformatics 07-21-2010, 11:35 PM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
Hi Cole, thanks for being *there* anyway....

Hi Cole,

thanks for being *there* anyway. Although i even tried to played around with the command line parameters to narrow down the error source, I still and constantly receive the segmentation...
Forum: Bioinformatics 07-19-2010, 01:19 AM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
Hi Cole, first of all, thanks for the quick...

Hi Cole,

first of all, thanks for the quick bugfix! At a first glance, everything works fine now, at least i get no more duplicates. However i receive segmentation faults with almost any sample i...
Forum: Bioinformatics 07-16-2010, 02:59 AM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
Hi Cole, first of all, thanks for...

Hi Cole,

first of all, thanks for engagement! I by the way don't think it necessary to apologize for being in BETA stage. IMHO the Trapnell-toolsuite is one of the most complete and consistent...
Forum: Bioinformatics 07-13-2010, 07:54 AM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
Thanks for your quick reply, oliviera. It...

Thanks for your quick reply, oliviera.

It is, however, the case that the transcript boundaries appear to not differ in their locations. Admittedly the RPKM values do actually differ with regard to...
Forum: Bioinformatics 07-13-2010, 01:31 AM
Replies: 34
Views: 16,515
Posted By Uwe Appelt
Dear all, i just encountering a very similar...

Dear all,

i just encountering a very similar problem. I ran cufflinks 0.8.3 on several samples, e.g.:

cufflinks --num-threads 8 --max-mle-iterations 10000 --GTF...
Forum: Bioinformatics 06-29-2010, 02:00 PM
Replies: 19
Views: 5,581
Posted By Uwe Appelt
Hi cczhong, the smart idea practically any...

Hi cczhong,

the smart idea practically any color-space aligner is built on, is not to translate the color-space reads into base-space in order to do the mapping/alignment, but to translate the...
Forum: Bioinformatics 04-29-2010, 10:41 PM
Replies: 19
Views: 5,581
Posted By Uwe Appelt
Hi Amadeur, thanks for your reply. According...

Hi Amadeur,

thanks for your reply. According to figure 1 (and result paragraph 1), SplitSeek splits every read into two related subreads and also leaves a gap between these two. I'm afraid, this...
Forum: Bioinformatics 04-29-2010, 10:57 AM
Replies: 1
Views: 1,417
Posted By Uwe Appelt
try these: 1) cisRED: Databases of...

try these:

1)
cisRED: Databases of genome-wide regulatory module and element predictions
http://www.cisred.org/

2)
TRANSFAC tools @ http://www.gene-regulation.com/

3) and additionally,...
Showing results 1 to 25 of 27

 


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