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Forum: Bioinformatics 08-11-2010, 03:48 AM
Replies: 0
Views: 1,308
Posted By syslm01
tophat islands information

Hi all,

I want to check the islands information identified by tophat, but I didn't find it in its tmp file. Does anyone know how to find it ?

Thank you very much.
Forum: Bioinformatics 07-23-2010, 01:18 AM
Replies: 1
Views: 901
Posted By syslm01
coverage file

Hi all,

I use tophat to analyze one dataset with 27bp length, and I am confused about the coverage.wig file it generated.

Here is one example:

chr1 11116146 11116147 47...
Forum: Bioinformatics 07-16-2010, 10:19 PM
Replies: 2
Views: 1,380
Posted By syslm01
I used the TopHat v1.0.13 and cufflinks v0.8.2...

I used the TopHat v1.0.13 and cufflinks v0.8.2 version.
Forum: Bioinformatics 07-16-2010, 08:13 AM
Replies: 2
Views: 1,380
Posted By syslm01
cufflink assemble result

Hi everyone,

I used tophat and cufflinks to assemble RNA-seq data. The result is good when the reads coverage is high. But I am confused the result when reads coverage is low. I attatched an...
Forum: RNA Sequencing 05-29-2010, 08:59 AM
Replies: 21
Views: 5,524
Posted By syslm01
hi ychen, here is the link...

hi ychen,

here is the link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20846
GSE20846_RAW.tar contains the SAM and gtf files
Forum: RNA Sequencing 05-29-2010, 07:34 AM
Replies: 21
Views: 5,524
Posted By syslm01
Hi, you could find the SAM file in their...

Hi,

you could find the SAM file in their suplemental material online.
Forum: RNA Sequencing 05-27-2010, 07:36 AM
Replies: 21
Views: 5,524
Posted By syslm01
Hi, I am also not sure about the other...

Hi,

I am also not sure about the other datasets: ftp://ftp.ncbi.nlm.nih.gov/sra/static/SRX019/SRX019275
The SRR039999_1.fastq.gz and SRR039999_2.fastq.gz are paired reads, but I am not sure the...
Forum: RNA Sequencing 05-27-2010, 04:39 AM
Replies: 21
Views: 5,524
Posted By syslm01
Hi fennan, I checked their command line,...

Hi fennan,

I checked their command line, they use mm9+wold_spikes as references and provide tophat with junction file pooled_200bp_frags.juncs. I'm not sure what these files are, I think that my...
Forum: RNA Sequencing 05-27-2010, 02:59 AM
Replies: 21
Views: 5,524
Posted By syslm01
Hi, did you use the datasets to run tophat...

Hi,

did you use the datasets to run tophat and cufflinks ? did the result are same as their provided sam files? I have a try, but my result is different.
Forum: RNA Sequencing 05-26-2010, 07:25 AM
Replies: 21
Views: 5,524
Posted By syslm01
Hi pascal and fenan, I received a letter...

Hi pascal and fenan,

I received a letter from SRA. Here is the reply:

In the case with SRX017794 and runs SRR037945 and SRR037946 we had a situation when SPOT_DESCRIPTOR has incorrect.
To...
Forum: RNA Sequencing 05-24-2010, 04:50 AM
Replies: 21
Views: 5,524
Posted By syslm01
Hi kmcarr, I will send an email to SRA. ...

Hi kmcarr,

I will send an email to SRA.

Thanks for your help.
Forum: RNA Sequencing 05-23-2010, 06:44 PM
Replies: 21
Views: 5,524
Posted By syslm01
hi john, I have checked some two paired-end...

hi john,
I have checked some two paired-end reads file, one reads in the file is like:


the sequence length is 152bp, and I know their RNA-seq data is 75bp, so I wonder if these two paired-ended...
Forum: Bioinformatics 05-23-2010, 06:27 PM
Replies: 0
Views: 1,261
Posted By syslm01
Unhappy cufflinks error

Hi,

I used tophat to alignment our pair-ended RNA-seq datasets and use cufflinks to do assemble, but an error occurred when we run cufflinks:

"Error: nonsense gene merge, exiting"

dose...
Forum: RNA Sequencing 05-21-2010, 06:43 AM
Replies: 21
Views: 5,524
Posted By syslm01
about SRA paired datasets

Hi everyone,

I have a question about pair-ended RNA-seq datasets on SRA. Some sequences file of pair-ended datasets are like SRR0011_1, SRR0011_2 which means these are paired sequences. But I...
Forum: Bioinformatics 05-14-2010, 07:12 AM
Replies: 0
Views: 1,619
Posted By syslm01
problem of tophat gff file

Hi all,

I try to use tophat GFF option, but met some problems. I downloaded the gtf format of Refseq genes from UCSC, and then convert it to gff3 format. But when I feed tophat this file, it...
Forum: Bioinformatics 05-05-2010, 03:43 AM
Replies: 0
Views: 1,284
Posted By syslm01
cufflinks assemble

Hi everyone

I assembled my RNA_seq data using tophat and cufflinks. But the assemble result seems strange. The length of exons were very short and most time, one transcript only contains one exon....
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