Forum: Bioinformatics
10-31-2015, 12:49 PM
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Replies: 12
Views: 2,577
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...
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Forum: Bioinformatics
10-31-2015, 02:32 AM
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Replies: 12
Views: 2,577
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...
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Forum: Bioinformatics
09-28-2015, 04:37 AM
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Replies: 12
Views: 2,577
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...
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Forum: Bioinformatics
02-03-2014, 03:28 PM
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Replies: 0
Views: 935
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 ...
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Forum: Bioinformatics
11-10-2011, 01:27 AM
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Replies: 12
Views: 6,004
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Forum: Bioinformatics
12-06-2010, 10:33 AM
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Replies: 31
Views: 7,846
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Forum: Bioinformatics
12-06-2010, 02:40 AM
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Replies: 31
Views: 7,846
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. ...
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Forum: Bioinformatics
11-23-2010, 06:23 AM
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Replies: 1
Views: 3,204
I don’t know if this could be the same problem,...
I don’t know if this could be the same problem, but I have observed problems with the calculated FPKM values from cufflinks. I don’t know if it is a bug, but the values for a transcript can change,...
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Forum: Bioinformatics
11-17-2010, 05:02 AM
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Replies: 0
Views: 1,322
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...
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Forum: Bioinformatics
10-01-2010, 05:12 AM
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Replies: 0
Views: 1,677
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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