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Forum: De novo discovery 04-17-2013, 06:38 PM
Replies: 2
Views: 3,622
Posted By lzsph
UPDATED: Go to the...

UPDATED:

Go to the trinityrnaseq_r2013-02-05/trinity-plugins/rsem folder, find a script named "rsem-calculate-expression", open it with a text editor, at line 30, there is , change the "0" to...
Forum: RNA Sequencing 03-05-2013, 10:56 PM
Replies: 3
Views: 2,265
Posted By lzsph
Hi Michael, I also got our annotation file...

Hi Michael,

I also got our annotation file (not generated through Blast2GO pipeline) formatted into .annot format according to the Blast2GO's example. Besides the GO functional classification, can...
Forum: Bioinformatics 03-05-2013, 10:41 PM
Replies: 1
Views: 5,226
Posted By lzsph
I haven't used blastall before, I just used NCBI...

I haven't used blastall before, I just used NCBI BLAST+ 2.2.26.
For example, with the local blastx tool.

$blastx -db db_name -query input_file -out output -evalue evalue -outfmt "6 qlen"...
Forum: RNA Sequencing 11-09-2012, 08:09 PM
Replies: 2
Views: 2,237
Posted By lzsph
Got it!:) Thank you HESmith.

Got it!:) Thank you HESmith.
Forum: RNA Sequencing 11-08-2012, 09:24 PM
Replies: 2
Views: 2,237
Posted By lzsph
Question Primers for qPCR validation in non-model RNA-Seq

Hey guys,

Once we got differentially expressed (DE) genes using RNA-Seq, we need to do qPCR validation.

1.For a non-model plant, among the DE genes, maybe most of them are unknown. If you pick...
Forum: Bioinformatics 09-13-2012, 05:47 PM
Replies: 7
Views: 3,908
Posted By lzsph
Hi Luyi, On the manual page...

Hi Luyi,

On the manual page (http://tophat.cbcb.umd.edu/manual.html) of TopHat, it says " In TopHat 1.1.0, we began supporting Applied Biosystems' Colorspace format."

Personally, I'm not...
Forum: Bioinformatics 09-13-2012, 04:58 PM
Replies: 2
Views: 4,306
Posted By lzsph
Hi rexxi, Yes. You can convert .SRA files to...

Hi rexxi,

Yes. You can convert .SRA files to .fastq format, which can be done by using SRA Toolkit (http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software).

The similar question was...
Forum: Bioinformatics 09-12-2012, 05:28 AM
Replies: 7
Views: 2,852
Posted By lzsph
Hi areyes, Thank you very much. I will...

Hi areyes,

Thank you very much.

I will read the paper.

Yours sincerely,
Senhao
Forum: Bioinformatics 09-12-2012, 05:23 AM
Replies: 7
Views: 2,852
Posted By lzsph
Hi Simon, Thanks for your advice....

Hi Simon,

Thanks for your advice. Unfortunately, without that background, I don't know how to write such a script. I may need your help if you have time and I wish it will not bother you too much....
Forum: Bioinformatics 09-12-2012, 12:59 AM
Replies: 7
Views: 2,852
Posted By lzsph
Hi guys, I have similar situation with what...

Hi guys,

I have similar situation with what mht has.
Could anyone fix this problem?

Thanks.

Regards,

Senhao
Forum: RNA Sequencing 09-11-2012, 05:33 AM
Replies: 0
Views: 978
Posted By lzsph
Question deleted

The thread has been deleted by author.
Forum: General 08-21-2012, 05:53 AM
Replies: 6
Views: 2,290
Posted By lzsph
Iadin, The links are not available. Would...

Iadin,

The links are not available. Would you mind sharing this case study with us?

It'll be grateful.

Thank you.

lzsph
Forum: Introductions 07-18-2012, 02:24 AM
Replies: 0
Views: 540
Posted By lzsph
hello

Hello everyone, I'm very glad to be a member of SEQanswers. Currently, I'm working with HiSeq 2000 data.
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