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Search: Posts Made By: superligang
Forum: Bioinformatics 03-07-2011, 04:14 PM
Replies: 0
Views: 3,556
Posted By superligang
KEGG pathway gene association data

I am trying to manually calculate the pathway enrichment for some genes. I have downloaded the panther and reactome data files which have the pathway annotations for genes. However, I couldn't find...
Forum: Bioinformatics 03-02-2011, 02:24 PM
Replies: 3
Views: 2,431
Posted By superligang
I thought the sampling process adopted in...

I thought the sampling process adopted in cufflinks is random since it does not maximize the MLE analytically
Forum: Bioinformatics 03-01-2011, 02:34 PM
Replies: 3
Views: 2,431
Posted By superligang
Is it normal for cufflinks produce different results in multiple run

I have running cufflink on 0.9M paired end sam data of human RNA and gtf annotations.

The GTF annotations were constructed based on the Ensembl, UCSC gene and refseq dataset downloaded from UCSD...
Forum: Bioinformatics 01-07-2011, 12:24 PM
Replies: 7
Views: 3,777
Posted By superligang
I don't run experiments in biology either:) I...

I don't run experiments in biology either:)
I downloaded this DNA data, and I guess probably RNA-seq is different from DNA-seq. When I aligned some RNA-seq data, the two ends of a pair of read...
Forum: Bioinformatics 01-07-2011, 10:57 AM
Replies: 7
Views: 3,777
Posted By superligang
I don't know if I understand the insert size...

I don't know if I understand the insert size correctly, but I use insert size as the distance between the two farthest bases of the two ends of a pair of reads.
For read of 35bp long, the minimal...
Forum: Bioinformatics 01-07-2011, 10:31 AM
Replies: 7
Views: 3,777
Posted By superligang
Interesting, but I don't quite understand what...

Interesting, but I don't quite understand what scaffold means in this context.
I hope that soapsnp handles the overlapping part of the two ends of a pair of read reasonably.
Thank you.
Forum: Bioinformatics 01-05-2011, 03:34 PM
Replies: 7
Views: 3,777
Posted By superligang
Questions about soapaligner and soapsnp

I am using soapaligner+soapsnp to find SNVs in our pair-end DNA data. I read the online manual, and the tools have been running smoothly.

However, there are three things I am not sure about.
...
Forum: Bioinformatics 04-15-2010, 01:54 PM
Replies: 2
Views: 2,097
Posted By superligang
this is great, thank you.

this is great, thank you.
Forum: Bioinformatics 04-10-2010, 11:47 AM
Replies: 6
Views: 2,543
Posted By superligang
thank you for the hint

thank you for the hint
Forum: Bioinformatics 04-09-2010, 09:46 PM
Replies: 6
Views: 2,543
Posted By superligang
Thank you for the suggestions. I thought tophat...

Thank you for the suggestions. I thought tophat used bowtie to map reads to existing known transcriptome, didn't know it could also uncover unknown transcript isoforms.

Quoted from tophat manual,...
Forum: Bioinformatics 04-09-2010, 05:42 PM
Replies: 6
Views: 2,543
Posted By superligang
Looking for an aligner allowing intron gap

We are mapping some RNA-seq data to the hg19 reference genome sequence. We used blat, which allows 750,000 as the intron size in default, but it was a little slow possibly due to the lack of...
Forum: Bioinformatics 04-07-2010, 02:26 PM
Replies: 2
Views: 2,097
Posted By superligang
The format of the ooc file in Blat

Hi, I'm new here.

Blat produces ooc file to store the over-repetitive fragment in the chromosomes. I wonder whether the format specification of this ooc file is public, or there is any program to...
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