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Forum: Bioinformatics 04-02-2016, 03:47 PM
Replies: 0
Views: 1,012
Posted By man4ish
Can't extract experiment accession using entrez query

Hi,

I am trying to use following query but i could not get this.

esearch -db SRA -query "biomol rna [PROP] AND Homo sapiens [orgn:__txid9606] AND (RNA-seq or rnaseq)" | efetch -format xml |...
Forum: Bioinformatics 04-08-2015, 04:01 AM
Replies: 0
Views: 1,289
Posted By man4ish
How to calculate LD in 2 direction?

Hi,

I have list of snps in vcf format and i need to calculate LD in such a way that window should be +_90 either side.

I tried both plink and vcf-tools but both works in forward direction(i.e...
Forum: Bioinformatics 02-15-2015, 01:23 AM
Replies: 2
Views: 2,023
Posted By man4ish
How to annotate vcf file using annovar?

Hi,

How can i annotate vcf file using Annovar?

I used following command but i found no output and all input goes to invalid file.

perl annotate_variation.pl -buildver hg19 ../input.vcf ...
Forum: Bioinformatics 04-20-2014, 06:17 PM
Replies: 1
Views: 1,162
Posted By man4ish
Open source tools for whole genome analysis.

HI,

I am newbie to genomics data analysis. I found BWA, SAMTools and GATK are good tools for SNV deteciotn but May i know what are open source tools for structural variant detection.

Thanks
Forum: Bioinformatics 04-18-2014, 07:21 PM
Replies: 7
Views: 1,811
Posted By man4ish
How can i post a question on this forum?

How can i post a question on this forum?
Forum: General 01-11-2014, 10:29 PM
Replies: 4
Views: 2,302
Posted By man4ish
OPen source pipeline for whole genome analysis of ABI reads

Hi,

Is there any open source pipeline for whole genome data analsyis? I need to start fro scratch and move to end solution.

Regards
Forum: General 01-11-2014, 10:18 PM
Replies: 4
Views: 2,302
Posted By man4ish
OPen source pipeline for whole genome analysis of ABI reads

Hi,

Is there any open source pipeline for whole genome data analsyis? I need to start fro scratch and move to end solution.

Regards
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