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Forum: Bioinformatics 11-19-2013, 04:30 AM
Replies: 2
Views: 355
Posted By fgh1124
Thanks for your reply. UNfortunately, I could...

Thanks for your reply. UNfortunately, I could found the line started with "@831".
Forum: Bioinformatics 11-19-2013, 04:16 AM
Replies: 2
Views: 355
Posted By fgh1124
TopHat (v2.0.4)error

[2013-11-19 07:32:34] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2013-11-19 07:32:34] Checking for Bowtie
Bowtie version: 0.12.7.0
[2013-11-19 07:32:34]...
Forum: Bioinformatics 07-11-2012, 06:10 PM
Replies: 1
Views: 671
Posted By fgh1124
How to calculate gene expression level

Hi, everyone!
I have the gtf annotation for mouse genome and rna-seq mapping to genome result(sam/bam). I want to know whether a software could calculate the genes' expression level based on these...
Forum: Bioinformatics 03-04-2012, 04:32 PM
Replies: 2
Views: 2,799
Posted By fgh1124
Help! How to calculate gene expression level (RPKM) in RNA-seq experiment

HI, everyone!

I just want to know each gene's expression level not the transcript isoforms. I have alignment data formated in SAM/BAM and annotation file in gtf/gff/bed. Some genes position have...
Forum: Bioinformatics 01-31-2012, 11:57 PM
Replies: 2
Views: 612
Posted By fgh1124
if you do not use "--closure-search", The result...

if you do not use "--closure-search", The result is OK!
Forum: Bioinformatics 01-30-2012, 08:19 PM
Replies: 2
Views: 612
Posted By fgh1124
I also met this problem

I also met this problem. Waiting for senior guys give some suggestion.
Forum: Bioinformatics 05-30-2011, 06:06 PM
Replies: 8
Views: 1,455
Posted By fgh1124
I am sorry that I misunderstood you qeustion. I...

I am sorry that I misunderstood you qeustion. I guess your problem maybe is the samtools. You can check if it work correctly!
Forum: Bioinformatics 05-30-2011, 05:41 PM
Replies: 8
Views: 1,455
Posted By fgh1124
revise the script! ...

revise the script!
http://seqanswers.com/forums/showthread.php?p=42800#post42800
Forum: Bioinformatics 05-30-2011, 05:38 PM
Replies: 21
Views: 8,003
Posted By fgh1124
improperly sorted SAM ! you have to revise...

improperly sorted SAM !

you have to revise the merge script manually. Please give the sam file a head.
for version cufflinks_1.0.2, the line 544, you can revise like that:
header = '''@SQ...
Forum: Bioinformatics 05-30-2011, 04:56 PM
Replies: 5
Views: 2,462
Posted By fgh1124
I need some advices.

I hope the seasoned men give me some advices.
Forum: Bioinformatics 05-30-2011, 07:24 AM
Replies: 5
Views: 2,462
Posted By fgh1124
The test for cuffmerge

To whom it may concern,
Thanks for the excellent software. I have 8 mouse samples, and get the transcripts for each sample using cufflinks. When I use cuffmerge to merge each sample to one file, I...
Forum: RNA Sequencing 12-15-2010, 04:42 PM
Replies: 0
Views: 713
Posted By fgh1124
One question about Tophat

When I use Tophat to get the unqiue reads which just mapped to one location in the genome, I have any problems. When I get the sam file, I filter it with the criterion that the last column is...
Forum: Illumina/Solexa 03-23-2010, 04:24 PM
Replies: 1
Views: 1,979
Posted By fgh1124
Solexa history

Anyone could tell me the Solexa history? how many generations the Solexa has passed through?
Forum: General 01-28-2010, 04:40 PM
Replies: 12
Views: 2,646
Posted By fgh1124
I have also heard this matter! May be due to...

I have also heard this matter!

May be due to the principle of SOLiD more complex than the Illumina, and the chance to get error bases is greater.
Forum: Introductions 01-28-2010, 04:24 PM
Replies: 0
Views: 623
Posted By fgh1124
hello from Beijing

I am from Beijing Institute of Biotechnology
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