User: arup

gravatar for arup
arup340
Reputation:
340
Status:
Trusted
Location:
India
Website:
http://arupgsh.github.io/
Twitter:
arupgsh
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
2 years, 6 months ago
Email:
a*******@gmail.com

PhD student @ Institute of Life Science, Bhubaneswar

Posts by arup

<prev • 74 results • page 1 of 8 • next >
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Answer: A: Extracting allele, Genotype from VCF file
... Extracting genotype information using R. library(vcfR) vcf <- read.vcfR(vcf_file, verbose = FALSE ) gt <- extract.gt(vcf, element = c('GT'), as.numeric = TRUE) For python take a look at the following article. http://alimanfoo.github.io/2017/06/14/read-vcf.html ...
written 2 days ago by arup340
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Comment: C: Filtering of lncRNAs and mRNAs for Differential expression analysis from RNA-seq
... It will be a good idea to process them separately starting from alignment to DE. The following research article suggests a similar approach. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150628 ...
written 4 days ago by arup340
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Answer: A: Expanding Genomic Coordinates Using Bedtools
... import sys with open(sys.argv[1],"r")as bed: for line in bed: #cor=line.strip("\n").split(" ") cor=line.strip("\n").split("\t") for i in range(int(cor[1]),int(cor[2])): print(cor[0],i, ...
written 4 days ago by arup340
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Comment: C: Alignment using bwa mem throws segmentation error
... Use the `-v ` to get more details. ...
written 4 days ago by arup340
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Comment: C: help to generate 100% Stacked Bar Chart or a histogram
... You are looking for the 2nd example in this article. http://rgraphgallery.blogspot.com/2013/04/rg-stacked-bar-chart-number-and-percent.html ...
written 4 days ago by arup340
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Comment: C: how to compare two TF binding sites
... If you are planning to overlap multiple ChIP-seq region files and want all the overlapping and unique regions you can use [BedSect][1]. It utilizes Bedtools `multiIntersectBed` for the multiplicity calculation and provides each possible overlap (with region coordinates) combination as output. [1 ...
written 4 days ago by arup340
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Comment: C: Appropriate home kit GPU for bioinformatics calculations
... I only know a handful tool that utilizes GPU. Example: https://nvlabs.github.io/nvbio/nvbowtie_page.html ...
written 5 days ago by arup340
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Answer: A: BWA (mem, sampe, or aln) used in bam file
... Try `samtools view -H SRR1172709.sam|grep "CL:"` $ samtools view -H SRR1172709.sam|grep "CL:" @PG ID:bwa PN:bwa VN:0.7.16a-r1181 CL:bwa mem -t 10 -R @RG\tID:FLOWCELL1.LANE1\tPL:ILLUMINA\tLB:SINDIA\tSM:SRR1172709 ../../MTB_DATA//Ref_H37rv/h37rv.fa ../SRR1172709_1.fastq ../SRR1172709_2.fastq ...
written 5 days ago by arup340
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Comment: C: How to process paired end data (using fastq-dump) to get Fw and Rv files
... Check this thread for related answers https://www.biostars.org/p/222122/ . ...
written 5 days ago by arup340
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Comment: C: RNA-Seq data for Ovarian Cancers for a pilot experiment from public database
... Try [Biojupis][1]. [1]: https://amp.pharm.mssm.edu/biojupies/ ...
written 6 days ago by arup340

Latest awards to arup

Scholar 4 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Supporter 4 months ago, voted at least 25 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]

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