SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 23 of 23
Search took 0.00 seconds.
Search: Posts Made By: Pejman
Forum: SOLiD 01-05-2011, 02:04 AM
Replies: 5
Views: 3,079
Posted By Pejman
Hey guys, how did you end up with SOLiD SAGE? I'm...

Hey guys, how did you end up with SOLiD SAGE? I'm working with Human Genome, and I have the feeling that the program is not functioning well, esp. that it's sooo slow! Did you guys find some...
Forum: Bioinformatics 12-08-2010, 01:40 AM
Replies: 10
Views: 13,419
Posted By Pejman
I'm not using cufflinks anymore. But, I got it...

I'm not using cufflinks anymore. But, I got it working with GTF files. It works nicely with .bam outputs from tophat. I can't remeber exactly where this exact problem was coming from, but I guess it...
Forum: Bioinformatics 11-10-2010, 11:21 AM
Replies: 1
Views: 2,410
Posted By Pejman
Suspicious results from CuffDiff

Hey folks
I'm running CuffDiff from the release 0.9.2, for RNAseq. I use it with tophat, and Reference annotation for human data. Here's the simple running command:


cuffdiff --FDR 0.01 -N...
Forum: SOLiD 10-29-2010, 04:12 AM
Replies: 5
Views: 4,727
Posted By Pejman
Hi The last version I've used was 1.1.1 and...

Hi
The last version I've used was 1.1.1 and that supports CS data. I recommend you to just use the precompiled versions, if you have problem with compiling. I checked the source files for 1.1.2, the...
Forum: Bioinformatics 10-18-2010, 07:28 AM
Replies: 15
Views: 5,037
Posted By Pejman
Well, missing tags are not essential problem, cuz...

Well, missing tags are not essential problem, cuz you can't run cufflinks without them ;) With bowtie you can easily make a compatible format, the question is how much sense it makes to do so. The...
Forum: Bioinformatics 10-18-2010, 06:03 AM
Replies: 15
Views: 5,037
Posted By Pejman
Dear Cole Could you please elaborate how much...

Dear Cole
Could you please elaborate how much of a catastrophe would that be to use Bowtie -> Cufflinks instead of Tophat -> Cufflinks, particularly in case of no-new-junctions?

I'm using single...
Forum: SOLiD 10-18-2010, 05:53 AM
Replies: 5
Views: 4,727
Posted By Pejman
well, I'm working with human data, so ... but I'm...

well, I'm working with human data, so ... but I'm not looking for new junctions, so I'm running it using predefined junctions from RefSeq and --no-new-junctions option, both for Tophat and Cufflinks....
Forum: Bioinformatics 10-15-2010, 07:52 AM
Replies: 35
Views: 11,698
Posted By Pejman
Is there somebody with some clue on how to tune...

Is there somebody with some clue on how to tune TopHat parameters? I just made a new thread for it:
http://seqanswers.com/forums/showthread.php?p=27217#post27217
Forum: SOLiD 10-15-2010, 07:46 AM
Replies: 5
Views: 4,727
Posted By Pejman
Tuning TopHat parameters for SOLiD reads

Hi folks

The new TopHat 1.1.1, nicely handles SOLiD reads, and the results can be piped easily to Cufflinks to make up a RNAseq pipeline. However, the manual page says:



and there are no...
Forum: RNA Sequencing 10-15-2010, 01:28 AM
Replies: 6
Views: 3,571
Posted By Pejman
I havn't used UCSD genome browser myself, but as...

I havn't used UCSD genome browser myself, but as far as I heard it's more desirable to upload wiggle files there, since SAM is huge.
and about yor problem with the "*" ones, those are the reads...
Forum: RNA Sequencing 10-14-2010, 10:30 AM
Replies: 6
Views: 3,571
Posted By Pejman
Cufflinks accepts BAM, there should be some other...

Cufflinks accepts BAM, there should be some other problem, Do make sure that you're using the very last version though!
Forum: Bioinformatics 10-14-2010, 10:28 AM
Replies: 35
Views: 11,698
Posted By Pejman
I just ran Tophat -> Cufflinks with and without...

I just ran Tophat -> Cufflinks with and without GTF files on SOLiD colorspace data smoothly, thanks to the developers the new version works like a charm!
Forum: Bioinformatics 10-11-2010, 04:13 AM
Replies: 31
Views: 8,870
Posted By Pejman
Hi, thanks for the hint. Yeah I know that, but...

Hi, thanks for the hint. Yeah I know that, but apparently TopHat+colorspace has just been released in too much rush. It crashes on SOLiD data:
http://seqanswers.com/forums/showthread.php?t=7118...
Forum: Bioinformatics 10-08-2010, 04:33 AM
Replies: 31
Views: 8,870
Posted By Pejman
@Adam: I'm not interested in new splice...

@Adam:
I'm not interested in new splice junctions, just looking for differential expression of the known transcripts using Cufflinks. However, I kinda think that it would be still better to use...
Forum: Bioinformatics 10-08-2010, 02:44 AM
Replies: 31
Views: 8,870
Posted By Pejman
@ ldong Thanks for the nice link! I managed...

@ ldong Thanks for the nice link!

I managed to get around the problem, by manually adding the SQ headers to the sorted same file! They were dumped out during the SAM->BAM->sort->SAM process :D
...
Forum: Bioinformatics 10-07-2010, 10:33 AM
Replies: 31
Views: 8,870
Posted By Pejman
I have the same problem. I'm using...

I have the same problem. I'm using cufflinks-0.9.1.Linux_x86_64 and trying to get it to produce expression levels based on a GTF file. If I run it without a reference GTF file, it works fine, gives...
Forum: Bioinformatics 10-06-2010, 05:08 AM
Replies: 7
Views: 3,402
Posted By Pejman
yes that what I did, but the problem is that...

yes that what I did, but the problem is that there are loads of options for group/track/table and I don't find any single combination to look significantly more appealing. I'm looking for a detailed...
Forum: Bioinformatics 10-06-2010, 02:34 AM
Replies: 7
Views: 3,402
Posted By Pejman
where can I get reliable GTF annotation files?

I'm trying to get the GTF files for hg18, preferably at isoform level, from UCSC browser portal, in order to run with Tophat and cufflinks, but apparently I can't find such files there.
So far I've...
Forum: RNA Sequencing 10-04-2010, 08:37 AM
Replies: 15
Views: 6,583
Posted By Pejman
wow, cool I knew that it's gonna be released soon...

wow, cool I knew that it's gonna be released soon but, cool! We are not interested in new splice junctions, but Bowtie output does not fit to Cufflinks, so why not TopHat. :)
I'm now trying out...
Forum: Bioinformatics 10-04-2010, 06:32 AM
Replies: 7
Views: 2,010
Posted By Pejman
Hi jamessmith01. Did you manage to work out the...

Hi jamessmith01. Did you manage to work out the Bioscope .BAM files + Cufflinks pipeline?
I currently have a hard time choosing a reasonable pipeline for SOLiD csfasta files of a RNAseq experiment.
Forum: RNA Sequencing 10-01-2010, 06:36 AM
Replies: 15
Views: 6,583
Posted By Pejman
Seems nice but I guess NovoalignCS needs a...

Seems nice but I guess NovoalignCS needs a license.
Forum: RNA Sequencing 10-01-2010, 04:42 AM
Replies: 15
Views: 6,583
Posted By Pejman
TopHat-ers say that TopHat's is gonna be able to...

TopHat-ers say that TopHat's is gonna be able to handle colorspace data very soon.
Forum: SOLiD 07-28-2010, 05:46 AM
Replies: 19
Views: 5,832
Posted By Pejman
Hi I'm a newbie! trying to find DEG though...

Hi
I'm a newbie! trying to find DEG though RefSeq data from SOLiD platform. I'm trying to do the alignment with the SOLiD SAGE V 1.1.0 but it just doesn't work well. I get huge amount of messages...
Showing results 1 to 23 of 23

 


All times are GMT -8. The time now is 11:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO