Forum: Bioinformatics
07-07-2014, 05:07 PM
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Replies: 1
Views: 1,781
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Forum: Bioinformatics
06-30-2014, 08:45 PM
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Replies: 1
Views: 1,781
Breakdancer inaccurate output.
Hi Guys,
I have run Breakdancer on a mouse KO sample and got several lines containing intrachromosomal translocations but described as interchromosomal, i. e., CTX instead of ITX, according to...
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Forum: General
01-28-2013, 03:16 PM
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Replies: 24
Views: 135,331
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Forum: Bioinformatics
01-27-2013, 02:54 PM
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Replies: 6
Views: 1,647
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Forum: General
01-27-2013, 02:49 PM
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Replies: 24
Views: 135,331
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Forum: General
01-27-2013, 05:12 AM
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Replies: 24
Views: 135,331
Hi All,
My apologies if this is not the...
Hi All,
My apologies if this is not the right place to place this question but I am curious about this issue.
I started a thread on acknowledging posts on the site -...
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Forum: General
01-22-2013, 06:23 AM
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Replies: 0
Views: 7,902
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Forum: Literature Watch
01-21-2013, 03:36 PM
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Replies: 77
Views: 52,697
Hi Valeu,
Sorry to be so insistent in this...
Hi Valeu,
Sorry to be so insistent in this aspect. I re-run control-freec on an mpileup file of one my samples with and without BAF options and I found a few differences between both runs. First,...
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Forum: Literature Watch
01-18-2013, 03:00 PM
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Replies: 77
Views: 52,697
Thanks for your prompt answer. I understand. I...
Thanks for your prompt answer. I understand. I will anxiously wait for the next version, speed improvements and bug corrections are always good news.
Just to be clear, when you use a pileup file,...
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Forum: Literature Watch
01-17-2013, 07:44 PM
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Replies: 77
Views: 52,697
Hi Valeu,
This is Fernando again. I have...
Hi Valeu,
This is Fernando again. I have re-run Freec on one of my samples where I previously run CNA analysis from a SAM file (unsorted, I use the FR mateOrientation parameter). The difference ...
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Forum: Literature Watch
12-21-2012, 04:05 PM
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Replies: 77
Views: 52,697
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Forum: Literature Watch
12-20-2012, 02:51 PM
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Replies: 77
Views: 52,697
Hi Valeu,
I am using control-freec to detect...
Hi Valeu,
I am using control-freec to detect CNV and LOH in normal vs tumor samples (low pass whole genome).
I had no problems to run it at all. However, I would like to ask you a couple of...
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Forum: RNA Sequencing
12-07-2012, 04:32 PM
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Replies: 2
Views: 1,651
Hi Stephio,
Just a comment. I use a similar...
Hi Stephio,
Just a comment. I use a similar approach - no CleanSam step used - for exome capture analysis and got comparable results. IMHO, the protocol We are currently following is standard and...
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Forum: Genomic Resequencing
11-11-2012, 03:31 PM
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Replies: 1
Views: 1,175
Hi Navik,
Perform a QA/QC of your raw reads...
Hi Navik,
Perform a QA/QC of your raw reads first. Then, If a reference genome is available, I would align your raw sequences first using a read aligner such as bwa or bowtie. Bear in mind that...
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Forum: Bioinformatics
11-09-2012, 03:26 AM
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Replies: 4
Views: 3,663
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Forum: Bioinformatics
11-08-2012, 09:51 PM
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Replies: 4
Views: 3,663
Hi Filip,
The same problem here (end to end,...
Hi Filip,
The same problem here (end to end, MapQual all 0s. However, this only happened when --no-mixed --no-discordant options were used. Find the parameters below:
bowtie2 -p 6 --phred33 -N...
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Forum: Bioinformatics
11-06-2012, 12:35 AM
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Replies: 3
Views: 2,742
Hi Jane,
As you could tell from my previous...
Hi Jane,
As you could tell from my previous post, I had the same issue. I found a putative solution to your problem.
I understand you have aligned your files using novoalign and I do not know if...
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Forum: Bioinformatics
11-05-2012, 10:52 PM
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Replies: 3
Views: 2,742
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Forum: Bioinformatics
10-28-2012, 06:59 PM
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Replies: 0
Views: 2,269
Bowtie2 output options
Hi guys,
I have been trying to write unaligned (--un path) and aligned (--al path) reads from a Bowtie2 (Bowtie2 2.0.0-beta7) alignment without success. It is PE 100 bp Illumina exome data. If I...
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Forum: Bioinformatics
10-11-2012, 06:48 PM
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Replies: 31
Views: 9,659
[/QUOTE]
Hi Tankman,
Sorry for my late...
[/QUOTE]
Hi Tankman,
Sorry for my late reply. As previously discussed, find below the output from tophat fusion. It worked and I obtained the same output as before.
Have yo been able to solve...
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Forum: Bioinformatics
10-03-2012, 04:56 AM
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Replies: 31
Views: 9,659
Hi Tankman,
Q1: Yes, I tested the output of...
Hi Tankman,
Q1: Yes, I tested the output of that test-sample and I then processed my own.
Q2: Yes, I used tophat 2.0.3 for those reads and I am currently using TopHat 2.0.4. Unfortunately, I will...
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Forum: Bioinformatics
10-02-2012, 09:46 PM
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Replies: 31
Views: 9,659
Hi Tankman,
Find below my directory...
Hi Tankman,
Find below my directory structure:
Total 48K
32K drwxr-xr-x 2 fernandr hpcmimr 16K Jun 22 12:33 blast
0 -rw-r--r-- 1 fernandr hpcmimr 38M Jun 22 12:33 ensGene.txt
0...
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Forum: Bioinformatics
08-14-2012, 03:31 AM
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Replies: 5
Views: 5,592
Hi Guys,
I got a similar error message in...
Hi Guys,
I got a similar error message in regards to /fix_map_ordering: /usr/lib64/libz.so.1: no version information available . However, TopHat completes the run. As far as I understand, this...
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Forum: Bioinformatics
08-07-2012, 05:33 AM
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Replies: 5
Views: 9,480
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Forum: Bioinformatics
07-31-2012, 08:44 PM
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Replies: 24
Views: 5,348
Hi Sarah,
Your reads look as if they were...
Hi Sarah,
Your reads look as if they were produced with CASAVA v1.8, which reports Phred+33 Q-scores (Illumina 1.9/Sanger). If that is the case, removing the --phred64-quals option from the bowtie...
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