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Forum: Illumina/Solexa 06-06-2012, 11:25 AM
Replies: 2
Views: 2,593
Posted By fangquan
pros and cons of Illumina

For the Illumina technology, where is the sequencing error mainly from ? Can anyone give me some brief introduction on Illumina's technology, including their pros and cons ??

Thanks,

Quan
Forum: Bioinformatics 11-17-2011, 08:39 AM
Replies: 0
Views: 1,255
Posted By fangquan
Questions on cuffdiff and q-value

Question on Cuffdiff’s DE results.

Code:
Quote:
cuffdiff -p $NSLOTS -o cuffdiff_v110 Ensembl_59.gtf C_3732_hits.bam,C_6341_hits.bam,C_6356_hits.ba
m,C_6124_hits.bam,C_60PO_hits.bam...
Forum: Bioinformatics 11-16-2011, 08:23 AM
Replies: 3
Views: 3,812
Posted By fangquan
I have the same problem. Please read my post here...

I have the same problem. Please read my post here (http://seqanswers.com/forums/showthread.php?t=15571).
Forum: Site Feedback/Suggestions 11-16-2011, 08:16 AM
Replies: 11
Views: 9,035
Posted By fangquan
How to delete a post ?

Sorry I accidentally post the same thread many times, I was not able to figure out how to delete posts here. Can somebody teach me ?

Thanks very much,
Quan
Forum: Bioinformatics 11-16-2011, 08:00 AM
Replies: 0
Views: 1,037
Posted By fangquan
Questions on cuffdiff and q-value

Question on Cuffdiff’s DE results.

Code:
Forum: Bioinformatics 09-15-2011, 07:13 AM
Replies: 1
Views: 5,752
Posted By fangquan
cuffdiff q-value

Does anybody know how the q_value was calculated in cuffdiff ? The manual claims it's "The FDR-adjusted p-value of the test statistic".
Forum: Bioinformatics 09-05-2011, 12:29 PM
Replies: 7
Views: 2,949
Posted By fangquan
cuffdiff replicates empty results

I use cuffdiff to detect differential expressed genes in two samples, since each has 2 replicates, so i use commas to separate replicates.

cuffdiff -m 40 genes.gtf /60PO/accepted_hits.bam ,...
Forum: Bioinformatics 08-16-2011, 11:32 PM
Replies: 42
Views: 19,337
Posted By fangquan
Hi, Sorry but I don't understand what do you...

Hi,

Sorry but I don't understand what do you mean "incompatible". I used the annotation from UCSC, the cuffdiff does give me some differential test results, and there is not big error reported.
...
Forum: Bioinformatics 08-16-2011, 10:33 PM
Replies: 42
Views: 19,337
Posted By fangquan
Hi Dario, You are right. But if you don't...

Hi Dario,

You are right. But if you don't go through compare step, you are still able to get some results from cuffdiff like this:

Performed 3204 isoform-level transcription difference tests...
Forum: Bioinformatics 08-16-2011, 10:20 PM
Replies: 0
Views: 1,721
Posted By fangquan
cufflinks results

I'm wondering what the results of cufflinks mean.

This is how they explaned:

In the transcripts.gtf, each row represents either a transcript or an exon within a transcript.

The...
Forum: Bioinformatics 08-16-2011, 07:55 PM
Replies: 42
Views: 19,337
Posted By fangquan
About the Cufflinks / Cuffdiff problem

Hi all,

I was able to run:

cuffdiff -o ./cuffdiff refGene_chr1.GTF B6341/hg19_chr1_seg/accepted_hits.bam 4242/hg19_chr1_seg/accepted_hits.bam


the refGene_chr1.GTF was downloaded from...
Forum: Bioinformatics 08-12-2011, 07:09 AM
Replies: 5
Views: 1,950
Posted By fangquan
Hi, Thanks for your reply, but I thinks it's...

Hi, Thanks for your reply, but I thinks it's already sorted. This is what I saw from cufflinks manual.

"The SAM file supplied to Cufflinks must be sorted by reference position. If you aligned...
Forum: RNA Sequencing 08-10-2011, 12:38 PM
Replies: 27
Views: 47,702
Posted By fangquan
Hi friend, I have two questions. (1) Is...

Hi friend,
I have two questions.

(1) Is there a way to see the command lines ran behind Galaxy's web-interface?
(2) A few jobs are still waiting to run, if I shut down my PC. Is it still...
Forum: RNA Sequencing 08-10-2011, 10:36 AM
Replies: 1
Views: 1,367
Posted By fangquan
Need urgent help for Tophat + Cufflinks !!!

Hi folks,

I'm running tophat (tophat -o output_dir a_ref a.fq) for alignment and cufflinks (cufflinks -o output_dir accepted_hits.bam) for assembles transcripts. The reads are single-end, 40-bp...
Forum: Bioinformatics 08-10-2011, 08:02 AM
Replies: 5
Views: 1,950
Posted By fangquan
Thanks, The read length is 40 bp. I will...

Thanks,

The read length is 40 bp. I will try out your suggestion.
Forum: Bioinformatics 08-10-2011, 07:55 AM
Replies: 5
Views: 1,950
Posted By fangquan
Thanks, The read length is 40 bp. I will...

Thanks,

The read length is 40 bp. I will try out your suggestion.
Forum: Bioinformatics 08-09-2011, 01:09 PM
Replies: 5
Views: 1,950
Posted By fangquan
Need urgent help for Tophat + Cufflinks !!!

Hi folks,

I'm running tophat (tophat -o output_dir a_ref a.fq) for alignment and cufflinks (cufflinks -o output_dir accepted_hits.bam) for assembles transcripts. The reads are single-end.

This...
Forum: RNA Sequencing 07-29-2011, 08:18 PM
Replies: 1
Views: 1,141
Posted By fangquan
Is anybody developing some RNA-Seq softwares?

I'm looking for some bioinformatics software development chances. If anybody is doing some RNA-Seq (not necessary related to RNA-Seq, broadly bioinformatics fine too). Here is a volunteer happy to...
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