Sourav Nayak

11 Questions 12 Answers 0 Followers

Questions related from Sourav Nayak

How to fill the gap between two contigs?

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 3,603 3 View

How to analyze BCFTools RoH output? How to provide information of in-house alternate allele frequency?

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 1,614 1 View

Can anybody help me in understanding one variant reported in 1000Genomes phase three release?

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 9,471 4 View

What if anyone removes all the unknown (or confusing) contigs from the reference genome (eg hg19) before alignment and other consecutive tasks?

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 431 2 View

Is there any server for in-del effect prediction?

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 2,913 3 View

What is the minimum read depth one should consider to confirm one postion to be covered?

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 5,214 3 View

What is the direction of paired-end reads?

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 927 3 View

What is the strategy to deal with adapter contamination inside the reads but not at either of the ends (3' or 5')?

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 7,307 12 View

How does SAMtools calculate consensus quality, SNP quality and RMS mapping quality?

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 5,927 1 View

How to get functional annotation data from a protein sequence?

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 9,239 4 View

Algorithm to find adapter contamination within the Illumina read dataset. Any suggestion?

Is there any algorithmic approach to find the adapter traces within the reads efficiently.

03 January 2013 7,895 15 View