User: vivekruhela

gravatar for vivekruhela
vivekruhela10
Reputation:
10
Status:
New User
Location:
Last seen:
2 months, 1 week ago
Joined:
7 months, 2 weeks ago
Email:
v**********@gmail.com

Posts by vivekruhela

<prev • 39 results • page 1 of 4 • next >
0
votes
0
answers
1.7k
views
0
answers
Comment: C: How To Import Tsv-File In Gene Ontology Or Annotate-It?
... I have obtained `.tsv` file from "virtual-Normal Correction" method which gives us somatic mutations.Can anyone suggest me how to annotate this file? Thanks ...
written 11 weeks ago by vivekruhela10
0
votes
1
answer
355
views
1
answers
Comment: C: Simple count of dbSNP (rs...) from .vcf file
... Please write it as an answer and close it so that others can easily find it and get help from. Thanks for providing better solution. ...
written 4 months ago by vivekruhela10
0
votes
1
answer
1.1k
views
1
answers
Comment: C: filtering pindel results
... Hi, Actually, I don't get it. In my pindel output file, I also got numerous entries. If I try your way, then I got 16,824 entries out of 1,44,563. Definitely, it is very less as compared to original one. But there are many 0/0 which are either INS or DEL, then how can I remove them. What will you ...
written 5 months ago by vivekruhela10
0
votes
0
answers
162
views
0
answers
Information about control data
... Hi, I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation detection (with the help of mutect or SomaticSnipper etc) with tumor data. Here are the questions ...
genome next-gen sequence sequencing written 5 months ago by vivekruhela10
0
votes
3
answers
449
views
3
answers
Comment: C: How to combine multiple tools to detct SVs in WES data
... Sorry I have again one more question: Is it ok to combine two gVCF files. One from Haplotype and another from Unifiedgenotype. I think it may be ok because both are complete files (i.e. consensus call) contains record from each position. So can we do this. Thanks. ...
written 5 months ago by vivekruhela10
0
votes
1
answer
251
views
1
answers
Comment: C: How to determine high-quality somatic mutations
... Hey, sorry for very late response again. The link sent by you for nature paper, author has used controlled data but the difference is author has used control data of difference patient and tumor data of different and then used optimization technique for fitness function stabilization. And that contr ...
written 5 months ago by vivekruhela10
0
votes
0
answers
204
views
0
answers
How to get unique somatic mutations for each individual patients
... Hi, I apologize if it is too simple question but I got stuck here. Here is the situation: I have exome data 32 patients. My aim is to identify unique somatic mutations in each patients. For this I have completed my pipeline for Whole Exome Data analysis using various tools like BWA mem, picard, ga ...
gene R next-gen sequence snp written 5 months ago by vivekruhela10
0
votes
2
answers
3.5k
views
2
answers
Comment: C: Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score doe
... I have a doubt in the command suggested by you. `-f` stands for only taking those reads. So if you have written `-f 0x02` that means reads associated with all other flags will be discarded and only `0x02` associated reads will be considered. Then there is no need of mentioning those flag whose assoc ...
written 5 months ago by vivekruhela10
0
votes
0
answers
307
views
0
answers
Comment: C: Percentage of uniquely mapped reads
... Thanks. I'll check it. ...
written 5 months ago by vivekruhela10
0
votes
1
answer
2.5k
views
1
answers
Comment: C: should I merge fastq files for different lanes before do QC?
... So you mean to say that it is OK to merge `S1_L001_R1_001.fastq` and `S1_L002_R1_001.fastq` because both are forward. Or I should do merging of `S1_L001_R1_001.fastq` (forward) and `S1_L001_R2_001.fastq` (reverse). I need your suggestions. I also want to know about cluster based analysis of fastq fi ...
written 5 months ago by vivekruhela10

Latest awards to vivekruhela

Supporter 5 months ago, voted at least 25 times.
Scholar 6 months ago, created an answer that has been accepted. For A: How to combine multiple tools to detct SVs in WES data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1808 users visited in the last hour