User: rocky.singh

gravatar for rocky.singh
rocky.singh50
Reputation:
50
Status:
New User
Location:
Last seen:
5 years, 2 months ago
Joined:
5 years, 6 months ago
Email:
r**********@xcelrislabs.com

about me

Posts by rocky.singh

<prev • 5 results • page 1 of 1 • next >
0
votes
4
answers
3.2k
views
4
answers
Answer: A: What Are The Best Practices For Snp Identification In Rna Seq Transcriptome Data
... Dear Concern, I have a query regarding snpEffect variant annotation analysis for castor bean (Ricinus communis) which is unavailable at snpEffect database. How could I make snpEffectPredictor.bin file for castor bean from its genome assembly fasta file available at JCVI http://castorbean.jcvi.org/d ...
written 5.4 years ago by rocky.singh50
0
votes
4
answers
3.2k
views
4
answers
Answer: A: What Are The Best Practices For Snp Identification In Rna Seq Transcriptome Data
... Hello I have a query regarding SNP vcf file called from SAMtools. ID and FILTER has no values in vcf file. How can we get SNP id for rice? When we do in human genome we refer dbSNP rsID using GATK VarAnnotaor, but in case of rice what should we refer. ...
written 5.4 years ago by rocky.singh50
2
votes
4
answers
52k
views
4
answers
Answer: A: What Does Samtools Flagstat Results Mean?
... I'm currently analyzing some RNAseq data for rice samples, and did alignment with BWA, removed PCR duplicates and later call SNPs with SAMtools on my paired-end files, I wanted to look at any form of program that could let me know how many reads from my dataset aligned, and how many of them properly ...
written 5.5 years ago by rocky.singh50 • updated 4.1 years ago by Leonor Palmeira3.6k
0
votes
4
answers
3.2k
views
4
answers
Answer: A: What Are The Best Practices For Snp Identification In Rna Seq Transcriptome Data
... ashutoshmits Thanking you for your speedy response. I have filtered raw data with prinseq and later aligned filtered fasta reads with BWA. Could you please suggest me which tool i.e. ANNOVAR , SNPeff should I use for annotating the SNP called. Rocky ...
written 5.6 years ago by rocky.singh50
4
votes
4
answers
3.2k
views
5 follow
4
answers
What Are The Best Practices For Snp Identification In Rna Seq Transcriptome Data
... I have 20 RICE RNA seq tranascriptome data hiseq 2000 platform paired end reads. I aligned fasta reads with BWA and remove PCR duplicates with PICARD. Later I call SNP with samtools using various parameters. I would like to clarify what parameters should I used while alinging to reference rice genom ...
variant snp rna-seq bwa written 5.6 years ago by rocky.singh50

Latest awards to rocky.singh

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1252 users visited in the last hour