17 Questions 18 Answers 0 Followers
Questions related from Sourav Nayak
SNP filtering remain as the essential step before performing any population genetic analysis. Can any expert share his/her experience on phylogenetic analysis with and without LD based SNP pruing...
27 March 2023 1,424 0 View
Hi everyone, We have sequenced genome of data of a comparatively less studied species using Pacbio long read sequencer. Now after initial assembly we compared the contigs with previous version...
26 June 2020 3,725 3 View
Currently I am working in a Transcriptomics lab and we are optimizing the RNA-Seq analysis pipeline to get best out of the data. We are counting the reads using bedtools against gene coordinates....
04 September 2018 2,679 5 View
Dear all, We have been working on QTL analysis for plant multi-parental population. As a initial stage we are going to perform bin mapping process for the population. Thus there is a need of...
18 October 2017 6,495 3 View
I have been trying to interpret the BCFTools output file for a single member of a small family. My aim is to find homozygous region with high confidence. With default command which is: bcftools...
03 November 2016 1,677 1 View
I am trying to write a program to annotate any VCF files against 1000 Genomes database. I have all the files with me. Now Surprisingly I have found out a variant which is : 1 207237233 . GGTGT...
29 December 2014 9,538 4 View
We have already performed whole exome sequencing using 62Mb kit. Now we want try 72Mb kit. I am keen to know what are the available kits that support run in Illumina HiSeq2500 platform. In this...
27 September 2014 7,873 1 View
A few days back we initiated sequencing run for multiplexed exome samples in HiSeq2500 platform. Due to human error cluster generation for reverse reads finished up as a disaster. So we will be...
10 July 2014 7,105 5 View
There are a good number of contigs in the hg19 release. The coordinates of this contigs are a bit confusing. Now if anybody want to keep these contigs out of reference before doing alignment, what...
12 February 2014 501 2 View
I got one deletion of single base in a particular gene which looks to be a frameshift deletion. Are there any server or software which can predict the effect of this deletion on the...
14 August 2013 2,981 3 View
While calculating coverage information from WES data one can find some regions covered with very less read depth (say 1,2 or 3). My question is what is the minimum cut-off one should consider to...
12 July 2013 5,262 3 View
I took a protein domain sequence from Uniprot database. My current aim is to design a structural model of this domain using a domain homologue with 25% sequence identity. Will it be a good choice...
08 June 2013 743 10 View
If we pickup same read from forward and backward read file. Are both of them moves from 5' -> 3' direction or they are opposite in direction?
27 March 2013 1,001 3 View
I have contamination of adapters inside the reads. Some part of the adapter sequences are found a few bases downstream or upstream of the 3' or 5' ends of the reads consecutively. How to deal with...
18 February 2013 7,372 12 View
While using SAMtools, consensus/variant calling used to give quality scores (eg. Consensus quality, SNP quality, RMS mapping quality). Can anyone suggest the computational logic behind these...
17 January 2013 5,989 1 View
I have a sequence of protein. Can anyone suggest me any pipeline using bioinformatics tools to get a prediction about the interaction pathway of the protein.
15 January 2013 9,297 4 View
Is there any algorithmic approach to find the adapter traces within the reads efficiently.
03 January 2013 7,963 15 View
