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Forum: Bioinformatics 11-15-2016, 08:43 AM
Replies: 0
Views: 1,076
Posted By RGP
Pindel "per sample" columns

Hello,

I am having trouble interpreting the Pindel "per sample" columns of the output files.
In a previous post it has been reported that lines 32+ are sample Id plus 6 values indicating:
1)...
Forum: Bioinformatics 05-15-2012, 08:45 AM
Replies: 2
Views: 1,580
Posted By RGP
Hello honey, you can find a detailed...

Hello honey,

you can find a detailed FusionAnalyser manual here:

http://nar.oxfordjournals.org/content/early/2012/05/08/nar.gks394/suppl/DC1

The manual is in File006.zip

About your...
Forum: Bioinformatics 05-15-2012, 04:35 AM
Replies: 2
Views: 1,580
Posted By RGP
Talking Announce new tool: FusionAnalyser

Dear all,

FusionAnalyser, a new graphical, event-driven tool tool dedicated to the identification of driver fusion rearrangements in human cancer through the analysis of paired-end...
Forum: Bioinformatics 07-12-2011, 02:51 AM
Replies: 4
Views: 5,670
Posted By RGP
Hello Gringer, thanks for your reply. What...

Hello Gringer,

thanks for your reply. What I'd like to highlight here is the difference between 'Unmapped' (i.e. SAM flag 0x0004 and 0x0008) and 'Not mapped in proper pair' (0x0002). The two...
Forum: Bioinformatics 07-10-2011, 01:11 AM
Replies: 4
Views: 5,670
Posted By RGP
Reads not mapped in proper pair: Bowtie output

Hello,

when I align paired end fastq reads mapping to two different chromosomes using BWA, I typically get this result:

ILLUMINA-8B7A89:1:33:5159:13399#TAGCTTA#0 65 chr22 21854387 37 30M chr9...
Forum: De novo discovery 11-29-2010, 04:03 AM
Replies: 4
Views: 4,739
Posted By RGP
Soap de novo .afg file

Hello Sunder,

to get the.afg you need to tell SoapDeNovo to generate it. In other words you need to turn the amos_file switch on (beware..the .afg it's a LARGE file):

./velvetg...
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