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Search: Posts Made By: Sam64
Forum: Bioinformatics 07-03-2014, 07:40 AM
Replies: 2
Views: 912
Posted By Sam64
upupupupupupupupupup :D

upupupupupupupupupup :D
Forum: Bioinformatics 06-26-2014, 02:55 AM
Replies: 2
Views: 912
Posted By Sam64
GATK forum

On GATK forum, you can read :

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthPerAlleleBySample.html

[...] Please note, however, that the AD...
Forum: Bioinformatics 06-26-2014, 02:10 AM
Replies: 2
Views: 912
Posted By Sam64
Why my variant is found if AD alt = 0 in my vcf file ?

Hi,

My problem is about intepretation of vcf file for indels variation, and particulary, about AD tag (Allele Depth) find in the last column. I obtained my vcf file after processing "Unified...
Forum: Bioinformatics 10-18-2012, 02:19 AM
Replies: 12
Views: 9,387
Posted By Sam64
Are you sure when you say it's probably better to...

Are you sure when you say it's probably better to keep all the reads....
Would anybody have an opinion about the problem ? Is it necessary to eliminate the reads with errors (MAPQ should be 0 for...
Forum: Bioinformatics 03-29-2012, 01:11 AM
Replies: 3
Views: 4,332
Posted By Sam64
Hi, You had an answer of Illumina ? ...

Hi,

You had an answer of Illumina ?

thank you to update if you had a solution :)

Sam

Paris, France
Forum: Bioinformatics 02-17-2012, 06:59 AM
Replies: 5
Views: 2,662
Posted By Sam64
up up up :)

up up up :)
Forum: Bioinformatics 02-13-2012, 07:46 AM
Replies: 5
Views: 2,662
Posted By Sam64
create windows10Kb.bed

Hi,

I try to find a way to create a bedfile in order to compute the coverage of aligned sequences on 10 kilobase “windows” spanning the genome.

chr1 0 10000
chr1 10000 ...
Forum: Bioinformatics 10-25-2011, 12:59 AM
Replies: 2
Views: 3,686
Posted By Sam64
Thank you for your post It helped me a lot :)

Thank you for your post
It helped me a lot :)
Forum: Bioinformatics 10-24-2011, 06:05 AM
Replies: 2
Views: 3,686
Posted By Sam64
Red face BWA aln _ option for number of mismatch ???

Hi,
What is the option which allows to select the number of mismatch accepted in a read? Please, anybody could help me by giving an example ?
Regards,
Sam64
Forum: Bioinformatics 10-20-2011, 05:11 AM
Replies: 2
Views: 2,461
Posted By Sam64
I use Partek genomic software but the licence is...

I use Partek genomic software but the licence is not free
Sam64
Forum: Genomic Resequencing 10-07-2011, 02:46 AM
Replies: 2
Views: 6,790
Posted By Sam64
Samtools mpileup_Paired Tumoral / Germline_keep only somatic mutations

I performed a genomic capture (Agilent technologie, SureSelect Target Enrichment System for Illumina Paired-end Sequencing) with paired tumoral and constitutional DNAs.
I created a .bam file for...
Forum: Genomic Resequencing 06-23-2011, 08:11 AM
Replies: 28
Views: 13,000
Posted By Sam64
DoubleA, Thank you for your link, the...

DoubleA,
Thank you for your link, the manuscript is very interesting but it just refers to the Illumina Sureselect protocol.
Has somebody some experience for the Agilent sureselect protocol ? in...
Forum: Genomic Resequencing 06-02-2011, 02:53 AM
Replies: 2
Views: 5,456
Posted By Sam64
I have just found a topic which gave me a...

I have just found a topic which gave me a possible answer...
Topic of NGSfan untitled Agilent SureSelect - coverage of high GC regions.

Apparently, as shown in the paper of Tewhey et al (2009...
Forum: Genomic Resequencing 06-01-2011, 06:47 AM
Replies: 2
Views: 5,456
Posted By Sam64
Coverage of reads not homogenous (sureselect target enrichement)

Hi all,

I have successfully run a targeted enrichment with SureSelect (Agilent protocol) . And now, I try to analyze the data. I need your help for the interpretation of sequencing...
Forum: Introductions 06-01-2011, 05:50 AM
Replies: 0
Views: 955
Posted By Sam64
hi everybody (sequence capture, DNA-seq)

Dear all,

I am really enjoy to join the SEQ community :)
I am novice in the domain of the sequencing.

I began to work with the sureselect target enrichment of Agilent technology. I used the...
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