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Search: Posts Made By: vang42
Forum: Bioinformatics 10-31-2015, 12:49 PM
Replies: 12
Views: 2,577
Posted By vang42
I am sure that many would actually use such a...

I am sure that many would actually use such a program if you wrote and released it to the community.

So far I have used a mixture of my own scripts with the consolidate.py script from this package...
Forum: Bioinformatics 10-31-2015, 02:32 AM
Replies: 12
Views: 2,577
Posted By vang42
Thank you blancha. As I see it, you method...

Thank you blancha.

As I see it, you method would collapse the reads in the last three UID3 reads, which is not the goal. I need to group together the same reads, that would be defined as...
Forum: Bioinformatics 09-28-2015, 04:37 AM
Replies: 12
Views: 2,577
Posted By vang42
Collapse PCR duplicates to a consensus read

We are working on methods to detect very low frequencies of mutations in cancer patients. By drawing a blood sample and isolating the plasma, we are able to detect very small amounts of circulating...
Forum: Bioinformatics 02-03-2014, 03:28 PM
Replies: 0
Views: 935
Posted By vang42
Problem with tophat2 handling strandedness

We are using tophat2 (v2.0.10) to analyze RNA-Seq samples produced by a stranded protocol. We have analyzed the same samples with and without a GTF file in the tophat run.

with GTF
@PG ...
Forum: Bioinformatics 11-10-2011, 01:27 AM
Replies: 12
Views: 6,004
Posted By vang42
Have you set TMP_DIR to a place with enough disk...

Have you set TMP_DIR to a place with enough disk space. You can set it using something lijke this: TMP_DIR=`pwd`/tmp or whatever you like.
Forum: Bioinformatics 12-06-2010, 10:33 AM
Replies: 31
Views: 7,846
Posted By vang42
Hi Sterding, That is strange. I am using Tophat...

Hi Sterding,
That is strange. I am using Tophat version 1.1.4 (beta, Linux x86_64 binary)
Bowtie version: 0.12.7.0
Samtools version: 0.1.8.0
And I reproduced your...
Forum: Bioinformatics 12-06-2010, 02:40 AM
Replies: 31
Views: 7,846
Posted By vang42
Hi sterding I have observed the exact same...

Hi sterding
I have observed the exact same thing and described it in http://seqanswers.com/forums/showthread.php?p=29933#post29933
I have reproduced your strange results using your files locally. ...
Forum: Bioinformatics 11-23-2010, 06:23 AM
Replies: 1
Views: 3,204
Posted By vang42
I donít know if this could be the same problem,...

I donít know if this could be the same problem, but I have observed problems with the calculated FPKM values from cufflinks. I donít know if it is a bug, but the values for a transcript can change,...
Forum: Bioinformatics 11-17-2010, 05:02 AM
Replies: 0
Views: 1,322
Posted By vang42
Cufflink's handling of reads

I am using Cufflinks to analyze RNAseq data and comparing different samples.
I run the programs with the following options:
cufflinks --num-threads 5 --GTF $ref_transcriptome --verbose --output-dir...
Forum: Bioinformatics 10-01-2010, 05:12 AM
Replies: 0
Views: 1,677
Posted By vang42
mapping of breakpoint

I have run some Illumina paired end and Illumina mate pair experiments, to analyze for chromosomal rearrangements in cancer genomics.

What is the best procedure to pinpoint the exact sequence just...
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