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Questions related from Sourav Nayak
We prepared un-stranded RNA-Seq library (SMART-Seq2) and sequenced in Illumina platform. We mapped with STAR (by adding XS tag) and assembled using cufflinks RABT assembly. Now after comparing...
12 December 2018 2,466 1 View
Currently I am designing a gene expression database in MySQL. Additionally I want give an web interface to the database, which is primarily for our lab use. And also I want to include some...
06 June 2018 6,401 2 View
We are working on a project where we need to perform genome wide association studies for multi-parental population. We have the SNP data from whole genome re-sequencing protocol. As I am quite...
10 October 2017 584 9 View
I have phenotype data and genotype data (DArT markers, SNP markers and SSR markers). My objective is to perform marker trait association study. I have found several R packages to perform...
08 August 2017 4,107 5 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...
11 November 2016 706 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...
12 December 2014 3,855 5 View
Rare complex disorders believed to be caused by combinatorial effect of many genes. Our lab works on one such disease. We are done with WES of four affected members from such a family. We are now...
08 August 2014 8,829 4 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...
02 February 2014 7,281 3 View
I am developing/refining a pipeline for exome data. According to reported articles there are mainly two callers I found out to be more acceptable among researchers: One is SAMTools' variant caller...
11 November 2013 867 5 View
I am looking for a vcf file of dbSNP release 131. Can anyone provide me with a link holding the data? Or is it possible to convert dbSNP flat files to vcf format by using any tool?
11 November 2013 7,869 7 View
I am trying to validate SAM file for further downstream processing using picard ValidateSAMFile command. But getting four types of error for ~50000 reads. Summary coming as: Error Type...
10 October 2013 5,536 4 View
I am trying to optimize the BWA+SAMTools/GATK pipeline for exome dataset. For the same purpose I need to know what is maximum memory BWA uses while executing aln and samse/sampe subroutine....
09 September 2013 8,998 1 View
I have modelled wild type and mutant structures, generated by comparative modelling. There is no significant change in secondary structures in mutants with respect to wild type. Though I am...
08 August 2013 263 1 View
I am trying to download detailed information about a genomic region, but not getting any way to download it. My requirement includes: intronic, exonic and both 3'-utr and 5'utr coordinates for all...
08 August 2013 2,732 6 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...
08 August 2013 9,990 4 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...
07 July 2013 1,067 3 View
Recently I have came to know a new term REFB. What is reference bias hypothesis in variant prediction from next generation sequencing data. Looking for your valuable inputs. Thanks in advance.
06 June 2013 2,932 0 View
If any read contains N (streaches of N), BWA usually replace it with any of four nucleotides randomly. My confusion is whether these replaced nucleotides are taken under consideration while...
05 May 2013 2,582 2 View
SAMTools finds PCR duplicates based on start and end position (in case of paired-end reads). I have a dataset of single end reads of variable length. Will SAMTools rmdup work on these to find out...
04 April 2013 639 10 View
I have an aligned file in bam format. I want to get back the reads from the aligned file. Looking for any tool that can serve the purpose in a precise manner. Is it a tricky process? Looking for...
04 April 2013 7,715 6 View
For Ion torrent data recommended algorithm is TMAP. Is it a published algorithm. If yes, can anyone provide me the link of publication?
03 March 2013 8,301 2 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?
03 March 2013 8,038 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...
02 February 2013 7,122 12 View
I am handling a few NGS datasets. While using samtools rmdup, sometimes it removes 10-15% of reads and sometimes 70-80% of reads. It is quite obvious that the second situation might have arisen...
02 February 2013 9,766 8 View
Is their any identifier within the sam files which can give me the number of reads aligned to a particular chromosomal region.
01 January 2013 7,160 3 View
Is there any algorithmic approach to find the adapter traces within the reads efficiently.
01 January 2013 2,616 16 View
I have a dataset of reads collected from Illumina platform.From these raw data I want to generate high quality read dataset. Can anyone suggest me any freely available softwares.
01 January 2013 998 6 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.
01 January 2013 4,083 5 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...
01 January 2013 1,545 1 View
While processing Illumnia paired-end reads, dataset of mine gave rise to both - paired-end and single-end due to read filtering based on phred score. Is there any way to map both dataset into the...
12 December 2012 8,100 5 View
