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Search: Posts Made By: sirmark
Forum: Bioinformatics 05-02-2013, 04:12 AM
Replies: 4
Views: 2,773
Posted By sirmark
I need to generate a small dataset of individuals...

I need to generate a small dataset of individuals organized in pool... with SNP and indel
is there a way to do this ?
Forum: Bioinformatics 05-02-2013, 01:06 AM
Replies: 2
Views: 1,108
Posted By sirmark
is there a way to generate the dataset ?

is there a way to generate the dataset ?
Forum: Bioinformatics 04-30-2013, 01:09 AM
Replies: 2
Views: 1,108
Posted By sirmark
some ideas ?

some ideas ?
Forum: Bioinformatics 04-16-2013, 01:49 AM
Replies: 3
Views: 2,742
Posted By sirmark
ok I solve from my link! thanks !

ok I solve from my link!
thanks !
Forum: Bioinformatics 04-16-2013, 01:39 AM
Replies: 3
Views: 2,742
Posted By sirmark
ok, I solve here: ...

ok, I solve here:
http://genome.ucsc.edu/cgi-bin/hgTables

but if I want start:end position of each gene,
what do I must select from the following ?
strand: + or - for strand...
Forum: Bioinformatics 04-16-2013, 01:28 AM
Replies: 3
Views: 2,742
Posted By sirmark
gene name and position list in a chr* of a genome

Hi all!

How can I obtain a list of gene on a chromosome ?

I need know the set of genes in chrX on hg18,
I would gene name, start:end position.

thanks for support!
Forum: Bioinformatics 04-15-2013, 04:29 AM
Replies: 2
Views: 1,624
Posted By sirmark
ok thanks! I'll see it!

ok thanks! I'll see it!
Forum: Bioinformatics 04-15-2013, 02:41 AM
Replies: 2
Views: 1,624
Posted By sirmark
tool for counting A T G C in a bam

Is there a tool to make counting of base in each position of reference genome ?

Example:
1 2 3 4 5 6 7
A C T T C G A :reference
A C G T A C A :read1
A A T T G C A :read2
A C G T G G A...
Forum: Bioinformatics 04-09-2013, 04:53 AM
Replies: 2
Views: 1,108
Posted By sirmark
download dataset pooled sample to testing SNP and indel calling

Hi all!

Where I download a bam file of a dataset with pooled sample, on which to do some test for SNP and indel calling ?

I have found this link:...
Forum: Bioinformatics 03-15-2013, 01:43 AM
Replies: 138
Views: 68,894
Posted By sirmark
I think it's important add in manual and in the...

I think it's important add in manual and in the wiki to add that vcf file, hg19.fasta
are in GATK bundle to which it's possible to access with an ftp client:
GATK budle ftp with an ftp client...
Forum: Bioinformatics 03-15-2013, 01:39 AM
Replies: 1
Views: 2,058
Posted By sirmark
I have solved by downloading vcf format from GATK...

I have solved by downloading vcf format from GATK budle ftp with an ftp client
http://gatkforums.broadinstitute.org/discussion/1215/how-can-i-access-the-gsa-public-ftp-server


I think that it's...
Forum: Bioinformatics 03-14-2013, 06:21 AM
Replies: 1
Views: 2,058
Posted By sirmark
[GATK] quality score recalibration -knowsite

Hi all!
I have a problem with a step of quality score recalibration, refererred to -knowsites.

when I try to run this command line:

java -Xmx4g -jar GenomeAnalysisTK.jar --num_threads 4 -l...
Forum: Bioinformatics 03-13-2013, 06:44 AM
Replies: 10
Views: 2,347
Posted By sirmark
just some questions : dindel is only for indel...

just some questions :
dindel is only for indel or also for snp ?

is there a reference/publication that compare different snp calling algorithms ?
Forum: Bioinformatics 03-13-2013, 06:43 AM
Replies: 5
Views: 1,857
Posted By sirmark
ok, thank you!

ok, thank you!
Forum: Bioinformatics 03-12-2013, 01:18 PM
Replies: 5
Views: 1,857
Posted By sirmark
--sample_ploidy 5 is the option to use ?

--sample_ploidy 5 is the option to use ?
Forum: Bioinformatics 03-11-2013, 03:17 PM
Replies: 5
Views: 1,857
Posted By sirmark
ok, I have corrected the request, that before was...

ok, I have corrected the request, that before was too specific
Forum: Bioinformatics 03-11-2013, 07:06 AM
Replies: 7
Views: 5,536
Posted By sirmark
can u define me what's a "downsample" ?

can u define me what's a "downsample" ?
Forum: Bioinformatics 03-11-2013, 06:04 AM
Replies: 7
Views: 5,536
Posted By sirmark
Have I undestand well -dcov usage ? If I...

Have I undestand well -dcov usage ?

If I want consider only reads with a specific coverage for an SNP calling process,
is it userful to use -dcov parameter ?
Forum: Bioinformatics 03-10-2013, 03:33 AM
Replies: 5
Views: 1,857
Posted By sirmark
GATK UnifiedGenotyper pooled sample

Hi!

How do I use UnifiedGenotyper in pooled samples ?

I have a bam file in which there are 5 individuals for each pool.

do GATK UnifiedGenotyper take into account of pooled sample ?
...
Forum: Bioinformatics 03-08-2013, 04:02 AM
Replies: 10
Views: 2,347
Posted By sirmark
ok! I understand. in your opinion, in case...

ok! I understand.

in your opinion, in case of pooled samples, which tools are the best ?
I'm finding an article with compared to evaluate this.
Forum: Bioinformatics 03-07-2013, 07:05 AM
Replies: 10
Views: 2,347
Posted By sirmark
thank you very very much, I'm confused less! ...

thank you very very much, I'm confused less!

I actually use IGV to see alignment of my BAM file to reference genome hg19.
To indel calling, I visualize manually each entire chromosome.

I'm...
Forum: Bioinformatics 03-07-2013, 07:02 AM
Replies: 10
Views: 2,347
Posted By sirmark
thank you very very much, I'm confused less! ...

thank you very very much, I'm confused less!

I actually use IGV to see alignment of my BAM file to reference genome hg19.
To indel calling, I visualize manually each entire chromosome.

I'm...
Forum: Bioinformatics 03-07-2013, 06:49 AM
Replies: 10
Views: 2,347
Posted By sirmark
for other analysis I mean always indel calling. ...

for other analysis I mean always indel calling.
Do IGV do indel calling ?


About GATK why is it possible to use DINDEL with -glm option ?

thanks for help!
Forum: Bioinformatics 03-07-2013, 05:44 AM
Replies: 10
Views: 2,347
Posted By sirmark
[general question]gatk, dindel, IGV

Hi all!
I'm newbie to analyzing NGS data and I'm not a biologist.

I'm very confused, and I have some question and hope that you can give me simple answer:

1th
Dindel is the GATK algorithm for...
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