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Forum: Bioinformatics 04-03-2014, 01:27 AM
Replies: 3
Views: 1,781
Posted By variadevang
Smile Thank You!

thanks a lot kbradnam. Appreciate the help!
Forum: Bioinformatics 04-02-2014, 02:19 AM
Replies: 3
Views: 1,781
Posted By variadevang
Question Using CEGMA

Hello Guys,
I have a project task, and i need to implement CEGMA for validating the predicted genes in the de-novo assembly. i have successfully installed and done a test run for CEGMA....
Forum: Bioinformatics 03-21-2014, 01:31 AM
Replies: 1
Views: 770
Posted By variadevang
Conver\

Hello All,
NGS data from SRA is downloaded in form of .sra files which are highly compressed and save a lot of space. fastq-dump converts .sra to fastq. i am interested in something which...
Forum: Bioinformatics 02-19-2014, 01:33 AM
Replies: 3
Views: 3,655
Posted By variadevang
grakocevic Thanks a lot for the...

grakocevic
Thanks a lot for the explanation. But i did not understand that if it filters, then why are the number of variant calls same as before recalibration?
Forum: Bioinformatics 02-14-2014, 04:11 AM
Replies: 3
Views: 3,655
Posted By variadevang
Unhappy Gatk vqsr

What does VQSR actually do? It improves the score? It filters the variants? or exactly what?
Is it an alternative for VariantFiltering based on hard values? i desperately need help on this.
p.s. i...
Forum: Bioinformatics 02-10-2014, 08:19 PM
Replies: 3
Views: 2,959
Posted By variadevang
Question Valid tools to use for Detecting SV/CNV in Whole Exome Data

I am working on whole exome data. i have 7 samples but no matching normal sample. i am to detect SV/CNV variant for these samples.
The sequencing platform is Illumina and i have BAM files ready for...
Forum: Bioinformatics 07-03-2012, 10:04 PM
Replies: 78
Views: 27,541
Posted By variadevang
is a 24GB RAM machine alright for aligning the...

is a 24GB RAM machine alright for aligning the .sai files using bwa sampe?????????
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