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Search: Posts Made By: ramujana
Forum: Illumina/Solexa 09-18-2016, 09:57 PM
Replies: 2
Views: 1,481
Posted By ramujana
Thanks Brian for insights.

Thanks Brian for insights.
Forum: Illumina/Solexa 09-15-2016, 09:54 PM
Replies: 2
Views: 1,481
Posted By ramujana
Intronic/intergentic variants using NGS WES

Hello folks,

Currently I'm looking for cost effective approaches to cover intronic and intergenic SNPs variants using Illumina NGS workflow? Some targeted enrichment protocol address that issue...
Forum: Bioinformatics 09-23-2015, 01:48 AM
Replies: 0
Views: 1,413
Posted By ramujana
MiSeq data analysis using Galaxy

Hi all,

I'm considering to analyse MiSeq resequencing FASTQ data (pair-end, adapter free) using Galaxy tools. Just to be sure my workflow-thinking is correct could you check these steps:
1....
Forum: Illumina/Solexa 09-16-2014, 10:35 PM
Replies: 3
Views: 1,951
Posted By ramujana
Minimum coverage info on Miseq

Hi,
does anyone can suggest how to extract MINIMUM coverage information of particular ROI after MiSeq run? (after standard fastq aligment to reference genome+manifest file and generating bam files)
Forum: Illumina/Solexa 04-09-2014, 01:48 AM
Replies: 1
Views: 1,571
Posted By ramujana
Coverage of ROI on TruSight

Hello,
i'm using Illumina TruSight Cancer panel and would like to get statastics how well was covered every gene/ROI. I'm using MiSeq Reporter for alignment and VarianStudio for variant (.vcf)...
Forum: Illumina/Solexa 10-11-2013, 11:02 PM
Replies: 44
Views: 22,637
Posted By ramujana
Dear All, i'm running TruSight Cancer Nextera...

Dear All,
i'm running TruSight Cancer Nextera Enrichment protocol for libraries (genomic DNA) on MiSeq and end up in quite low (although very good quality reads) cluster density 180K with 0,2N NaOH....
Forum: General 03-27-2013, 04:26 AM
Replies: 5
Views: 3,327
Posted By ramujana
BTW, i could also argue that simple Sephadex G50...

BTW, i could also argue that simple Sephadex G50 filled collums would also work for clean-up - any commens on this?
Forum: General 03-27-2013, 02:38 AM
Replies: 5
Views: 3,327
Posted By ramujana
Hello, i face the similar problem what to use...

Hello,
i face the similar problem what to use instead of Ampure (i'm dealing with 2x150bp reads on MiSeq, Nextera XT DNA prep and pooling amplicons). However, on the BC website i find information...
Forum: Ion Torrent 05-22-2012, 12:13 AM
Replies: 122
Views: 121,546
Posted By ramujana
Recently i've got a response from...

Recently i've got a response from LifeTechnologies representatives - what would be your comments regarding this:

Lomanís paper is very popular thanks to Illumina. However, we have some things to...
Forum: Ion Torrent 05-02-2012, 01:56 AM
Replies: 122
Views: 121,546
Posted By ramujana
Thank you all for the information. It seems i'm...

Thank you all for the information. It seems i'm leaning towards MiSeq.
Forum: Ion Torrent 04-23-2012, 07:59 AM
Replies: 122
Views: 121,546
Posted By ramujana
Ion Torrent PGM vs Illumina MiSeq

Hello all users,
recently i've received a grant and plan to purchase small scale NGS platform for targeted sequencing of human genome (germline mutations in hereditary cancer genes, in particular)....
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