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Forum: Bioinformatics 11-30-2015, 11:59 AM
Replies: 0
Views: 1,670
Posted By c_ro87
Illumina Truseq Pair end

Hello, I have data from a custom truseq design.

The reads alignment was done using BWA, and variant calling using GATK following the best practices.

From the image, the bottom panel shows the...
Forum: Bioinformatics 10-04-2014, 04:46 PM
Replies: 2
Views: 1,554
Posted By c_ro87
how i delette this?

how i delette this?
Forum: Bioinformatics 10-03-2014, 07:15 AM
Replies: 2
Views: 1,554
Posted By c_ro87
Help with a probably bad variant call

Hello all,

i have a variant from a ION PGM sequencing, called with the ION Torrent variant caller plugin

CHR POS ID REF ALT

chr22 44324726 . T TG
The flow...
Forum: Bioinformatics 05-28-2014, 06:24 AM
Replies: 0
Views: 1,070
Posted By c_ro87
Missing genotypes, in case control study using Plink

Hello,

I have a sequencing in ION PGM.

We sequenced 96 barcodes (individuals) and 310 amplicons (chromosomal regions).

32 barcodes are controls and 64 are cases.

We did the variant...
Forum: Ion Torrent 04-11-2014, 08:00 AM
Replies: 14
Views: 15,278
Posted By c_ro87
@arnaud83: how you do the strand bias filtering?

@arnaud83: how you do the strand bias filtering?
Forum: Ion Torrent 04-04-2014, 07:47 AM
Replies: 14
Views: 15,278
Posted By c_ro87
Hello, i'm analyzing Ampliseq runs on custom gene...

Hello, i'm analyzing Ampliseq runs on custom gene panels, using a 316 Chip

i also want to try something different, i also try the GATK, but after the MarkDuplicates step, i found that due to my...
Forum: Ion Torrent 04-04-2014, 07:41 AM
Replies: 2
Views: 5,967
Posted By c_ro87
Strand Bias filtering

Hello all,
i run the variantCaller in germline_low_stringency mode with the default parameters

the strand bias threshold for snp Strand Bias is 0.95, everything up that value is considered strand...
Forum: Illumina/Solexa 09-14-2012, 10:14 AM
Replies: 0
Views: 836
Posted By c_ro87
iScan system, sample dataset

Hi all, is there any example dataset for the iScan Illumina system?? i can't find anything

thx
Forum: Bioinformatics 09-14-2012, 10:12 AM
Replies: 0
Views: 783
Posted By c_ro87
Illumina iScan example data sets

Hello

is there any example dataset for the iScan Illumina system?

thx
Forum: Bioinformatics 05-07-2012, 12:19 PM
Replies: 0
Views: 664
Posted By c_ro87
ESTate sequence clustering software

Hi, where i can download this SW?

i can't find this...

thx in advance
Forum: Bioinformatics 02-22-2012, 08:10 AM
Replies: 0
Views: 1,248
Posted By c_ro87
get mate pair info from xml file

Hello i'm trying to assembly a sequencing done 100% with sanger reads, using celera assembler

i have the fasta, fasta.qual, anc, clip and xml files from NCBI Trace

the xml files have the mate...
Forum: Bioinformatics 02-10-2012, 10:20 AM
Replies: 1
Views: 1,124
Posted By c_ro87
Lost in fog, what to do with a assembly

Hello, i'm fairly new to the assembly world... maybe someone of u can give me a lead to where i must point. i'm a student and entry into a big assembly project, but my director not give me guidelines...
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