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Forum: RNA Sequencing 07-11-2012, 07:47 AM
Replies: 2
Views: 1,836
Posted By townway
yes,I used -g/--GTF-guide and also this was...

yes,I used -g/--GTF-guide

and also this was aligned by Tophat2.

Do you have any idea to modify the parameters?
Thank you in advance
Forum: RNA Sequencing 07-10-2012, 12:34 PM
Replies: 2
Views: 1,836
Posted By townway
Cufflinks parameter optimization

I used tophat2-cufflinks (latest version) to detect the transcripts and validate by experiments. I found one region (attached file, 100 bp length Hiseq, paired-end, human genome), cufflinks tends to...
Forum: Bioinformatics 05-24-2012, 02:42 PM
Replies: 2
Views: 4,501
Posted By townway
I have similar errors, [2012-05-24 16:47:41]...

I have similar errors,

[2012-05-24 16:47:41] Joining segment hits
[FAILED]
Error running 'long_spanning_reads':Loading insertions...Error: malformed insertion coordinate record
Forum: Bioinformatics 05-04-2012, 12:48 PM
Replies: 13
Views: 10,546
Posted By townway
yes, I have the same problem, it has been running...

yes, I have the same problem, it has been running for two days (48 hours), and no file updates in the tmp folder for last 10 hours..it seems to be stopped...

did you fix this problem?

Thanks
Forum: Bioinformatics 02-03-2012, 02:28 PM
Replies: 4
Views: 8,941
Posted By townway
The following are the output of...

The following are the output of picards_markduplicates, I changed some of the options to bigger number but it still give me error.
my file is about 10GB of bam file, and program was running with 24G...
Forum: Bioinformatics 01-11-2012, 08:46 AM
Replies: 24
Views: 14,887
Posted By townway
yes that is true, without them, it works well...

yes that is true, without them, it works well now.
Forum: Bioinformatics 01-11-2012, 07:28 AM
Replies: 24
Views: 14,887
Posted By townway
My data is around 200M reads from Hiseq one lane...

My data is around 200M reads from Hiseq one lane and I used 16 G memory to run Tophat 1.3.3 with coverage microexon butterfly search option.
Btw It worked well with old version of tophat
Forum: Bioinformatics 01-10-2012, 01:35 PM
Replies: 24
Views: 14,887
Posted By townway
I had the same problem today, hope someone can...

I had the same problem today, hope someone can stand out and point the way to fix.

My data directly output from illumina pipeline with two fastq files.
Forum: Bioinformatics 11-21-2011, 11:24 AM
Replies: 66
Views: 29,421
Posted By townway
yes dear, I am doing extactly the same :) ...

yes dear, I am doing extactly the same :)

but cisgenome(windows version) seems not like my PC, so I switched to linux version on our cluster and it worked.

I wonder it might be a bug of windows...
Forum: Bioinformatics 11-18-2011, 04:07 PM
Replies: 66
Views: 29,421
Posted By townway
Hi all, I am using latest Cisgenome (windows...

Hi all,

I am using latest Cisgenome (windows version) to call Chi-seq peaks. But I got the errors when I used "Two sample peak calling (New and recommend)". After I added my IP and input file in...
Forum: RNA Sequencing 09-06-2011, 01:32 PM
Replies: 13
Views: 4,851
Posted By townway
how about several treatments and also samples...

how about several treatments and also samples without replicates, does DEXSeq handle as well? Thank you
Forum: Bioinformatics 09-01-2011, 11:50 AM
Replies: 7
Views: 7,720
Posted By townway
would you mind which version of bamtools you...

would you mind which version of bamtools you used?
the current one does not have cigar filter
Thank you

General Filters:
-alignmentFlag <int> keep reads with this *exact*
...
Forum: Bioinformatics 09-01-2011, 09:33 AM
Replies: 7
Views: 7,720
Posted By townway
how can I calculate the number of reads mapped to...

how can I calculate the number of reads mapped to junctions by bamtools or picard?

a simple way I can think about is to counts the splitted reads, but I am not sure it is right way.

Thank you
Forum: RNA Sequencing 08-03-2011, 10:32 PM
Replies: 155
Views: 65,086
Posted By townway
Hi Xi, My data is time course data with 6 time...

Hi Xi,
My data is time course data with 6 time points but without replicate. I wonder if I can try your DEGseq.

If not, would you suggest some alternatively ways?

Thank you in advance!
...
Forum: Bioinformatics 07-08-2011, 07:51 AM
Replies: 5
Views: 4,650
Posted By townway
I also find the same problem, cuffmerge seems to...

I also find the same problem, cuffmerge seems to filter some of the isoforms.

anybody here can help me ?
cuffmerge-*.tmap missing
I am running cuffmerge to combine some of samples GTF files. And...
Forum: Bioinformatics 07-05-2011, 01:44 PM
Replies: 21
Views: 16,641
Posted By townway
I am running cuffmerge to combine some of samples...

I am running cuffmerge to combine some of samples GTF files. And error is showing as follow. Would you please tell me what I should do to fix the problem? Thank you so much!


$...
Forum: Bioinformatics 07-01-2011, 12:35 PM
Replies: 0
Views: 1,807
Posted By townway
cuffmerge-*.tmap missing

I am running cuffmerge to combine some of samples GTF files. And error is showing as follow. Would you please tell me what I should do to fix the problem? Thank you so much!


$...
Forum: RNA Sequencing 05-02-2011, 07:00 AM
Replies: 1
Views: 2,707
Posted By townway
I think bionomal test is better or you might have...

I think bionomal test is better or you might have to say you also detect imbalance in DNA level which is a little bit uncertain
Forum: RNA Sequencing 04-15-2011, 03:04 PM
Replies: 5
Views: 6,778
Posted By townway
I have not made it either...hope some one can...

I have not made it either...hope some one can provide answers
Forum: RNA Sequencing 04-11-2011, 07:29 AM
Replies: 6
Views: 3,819
Posted By townway
you might go to ucsc table browser to select the...

you might go to ucsc table browser to select the right categories and pull the annotations you want.

BTW, what aligner you use?
Forum: Bioinformatics 03-30-2011, 02:38 PM
Replies: 34
Views: 36,156
Posted By townway
Hi Simon, I am working on RNA-seq data and...

Hi Simon,

I am working on RNA-seq data and try to use you scripts to go over it. But my data is from cell lines which treated with drugs differing in time. I wonder whether DESseq can handle time...
Forum: Bioinformatics 01-11-2011, 08:56 AM
Replies: 27
Views: 7,715
Posted By townway
we had the same situation as well when we use...

we had the same situation as well when we use tags to do the CHIP
Forum: Bioinformatics 12-17-2010, 12:59 PM
Replies: 30
Views: 12,374
Posted By townway
Thank you Andrew. The main problem for me as...

Thank you Andrew.
The main problem for me as you said is the text editor messing everything up.
now it is running.
Forum: Bioinformatics 12-02-2010, 03:24 PM
Replies: 30
Views: 12,374
Posted By townway
would you share some your experience of defuse? ...

would you share some your experience of defuse?

when I modified config.txt like
# Directory where you have decompressed your dataset
dataset_dir =...
Forum: RNA Sequencing 12-01-2010, 08:41 AM
Replies: 6
Views: 3,819
Posted By townway
RSEQtools

Did anyone has experience with this package?

I have problem when I use "sam2mrf" to convert my sam file from TopHat to mrf format.

$ sort -r accepted_hits.sam | sam2mrf
Showing results 1 to 25 of 40

 


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