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Search: Posts Made By: songsy
Forum: Bioinformatics 03-31-2013, 05:19 PM
Replies: 38
Views: 12,075
Posted By songsy
adarob, I have a similar question. I first use...

adarob, I have a similar question. I first use tophat to get the bam file and then run cufflinks with --GTF command, which goes wrong with message like:
You are using Cufflinks v2.0.2, which is the...
Forum: Bioinformatics 12-18-2011, 09:46 PM
Replies: 0
Views: 2,930
Posted By songsy
how to do annotation on Breakdancer result

I've got some breakdancer results on SV. But the format is not in VCF. Beside, the outcome of breakdancer is an estimate of structural variation. It couldn't gave exact breakpoints, nor the sequence...
Forum: Bioinformatics 11-29-2011, 09:44 PM
Replies: 2
Views: 2,369
Posted By songsy
RDXplorer

I'm using SVmerge. One of the tools is RDXplorer. I run the run.sh. It first picked q0 items and write into a sam file. And then it uses samtools mpileup to call variants. But it doesn't work,...
Forum: Bioinformatics 11-03-2011, 08:29 PM
Replies: 3
Views: 1,853
Posted By songsy
Is it a software that can show paired end mapping?

I've tried samtools tview, but it only shows single read.
I want to look at the paired end mapping.
Thank you very much
Forum: Bioinformatics 10-26-2011, 05:54 AM
Replies: 32
Views: 16,253
Posted By songsy
Thank you very much. It works fine. I still...

Thank you very much. It works fine.
I still have some questions for the output of pindel:
1. the LI output has a different header and I don't quite understand. The attach is one output. I don't...
Forum: Bioinformatics 10-25-2011, 02:33 AM
Replies: 32
Views: 16,253
Posted By songsy
Sorry. I don't know which one contains the...

Sorry. I don't know which one contains the pindel2vcf converter on the downloads page. Could you tell me? Thank you very much.
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