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Forum: Bioinformatics 11-28-2012, 12:32 PM
Replies: 3
Views: 967
Posted By zhaowei
I mean, if junction area is intron area, tophat...

I mean, if junction area is intron area, tophat output and Cufflinks output should be consistent. But when I checked a gene, the intron area implied by Tophat and Cufflinks are different. Then I...
Forum: Bioinformatics 11-28-2012, 12:13 PM
Replies: 3
Views: 967
Posted By zhaowei
tophat output

From Tophat output "junctions.bed", we could know the position of junctions. I think this junction should be intron. But after I assembled tophat output by Cufflinks, I found that the position of...
Forum: Bioinformatics 11-04-2012, 07:58 PM
Replies: 2
Views: 1,499
Posted By zhaowei
You could download annotation from NCBI, if you...

You could download annotation from NCBI, if you just want to use it. ftp://ftp.ncbi.nih.gov/genomes/Fungi/
Forum: Bioinformatics 10-10-2012, 09:01 AM
Replies: 1
Views: 1,622
Posted By zhaowei
Alternative Splicing isoform Annotation

Hello

I am trying to identify differential alternative splicing events across two conditions. Now I plan to use MISO. This package requires a alternative splicing event gff annotation.

So far...
Forum: Bioinformatics 05-17-2011, 07:58 AM
Replies: 3
Views: 2,733
Posted By zhaowei
could you tell me which one should I select?

could you tell me which one should I select?
Forum: Bioinformatics 05-16-2011, 12:44 PM
Replies: 3
Views: 2,733
Posted By zhaowei
how to get annoation file from UCSC table browser?

hi all

Someone says we could use ucsc table brower, choose track and then refflat table. How to refflat table? Is there a tutorial or instruction?
Forum: Bioinformatics 01-31-2011, 01:04 PM
Replies: 1
Views: 2,535
Posted By zhaowei
how to identify paired end from qseq or fastq

I got data in qseq format. The description of this format says, column 7 is 1 for single read, 1 or 2 for paired end .

The problem is if the value is 1, it is impossible to indentify whether it is...
Forum: Bioinformatics 01-28-2011, 12:58 PM
Replies: 1
Views: 2,227
Posted By zhaowei
I think I have figured out

I think I have figured out
Forum: Bioinformatics 01-28-2011, 11:19 AM
Replies: 1
Views: 2,227
Posted By zhaowei
generate data from ewbt file

hi all

Now I have installed tophat 1.2.0,and downloaded homo sapien indexes. What should I do next? How to generate *.fa file?

thx
I have just begun to use tophat
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