User: arup

gravatar for arup
arup40
Reputation:
40
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Location:
India
Website:
http://www.wptron.com/
Twitter:
arupgsh
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Google Scholar Page
Last seen:
2 days, 15 hours ago
Joined:
2 years ago
Email:
a*******@yahoo.co.uk

JRF @ Institute of Life Science, Bhubaneswar

Posts by arup

<prev • 10 results • page 1 of 1 • next >
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Comment: C: installing bwa for linux 32 bits
... Try precompiled version. ...
written 2 days ago by arup40
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Answer: A: How many cell lines for RNA-seq comparisons?
... For transcript comparison b/w cell lines or differential gene expression analysis, it is recommended to have minimum two replicates and >30x coverage(paired end). If you also want to check splice variants then coverage should be >50x (paired end). ...
written 23 days ago by arup40
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Answer: A: circos plot gene expression by RNA-Seq
... The instruction will completely depend upon how you are planning to visualize the data. One way to visualize RNA-Seq data using circos is to mark the genes in chromosomes and add another circle repressing up regulation and download regulation using bars of different colors. Example : https://www.re ...
written 11 weeks ago by arup40
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Comment: C: Download list of all genes of genome build GRCh38.p0
... Use bioMart or UCSC TableBrowser. https://genome.ucsc.edu/cgi-bin/hgTables ...
written 12 weeks ago by arup40
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Answer: A: trimmomatic excution error
... Try to run like example mentioned in Trimmomatic homepage. http://www.usadellab.org/cms/index.php?page=trimmomatic For the mentioned scenario the command will be like `java -jar ~/software_library/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 4 -phred33 DRR001913_1.fastq DRR001913_2.fastq t ...
written 12 weeks ago by arup40
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Answer: A: How can I save a histogram in different widths and heights?
... What do you actually mean by different size? If it's the dimension you can save the same plot with different width and height by adding separate codes like following. png(filename = "my_plot.png", width = 480, height = 480, units = "px", pointsize = 12, bg = "white", antialias) png(filen ...
written 4 months ago by arup40
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Answer: A: Visualising BedGraph files on UCSC [custom tracks]
... The bedGraph file you have don't use the correct formatting. A standard bedGraph file will be like the following example. track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20 chr19 49302000 49302300 -1.0 ...
written 5 months ago by arup40
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Comment: C: rna seq bowtie couldn't find index files
... The output folder you specified should be followed by "-o" not "-0" and avoid spaces in directory/filenames. ~/Desktop/myecoli-rna seq/referecoli should be written as ~/Desktop/myecoli-rna\ seq/referecoli ...
written 9 months ago by arup40
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Comment: C: How to Download RNAseq-Clinical Follow up data of BRCA
... If you are asking for the TCGA dataset you can access it using [FireBrowse RESTful API][1]. [1]: http://firebrowse.org/api-docs/ ...
written 10 months ago by arup40
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Comment: C: TCGA: Does TCGA cancer studies have mRNA expression data for Control/Normal samp
... TCGA-Assembler out of service, any good alternative? ...
written 14 months ago by arup40

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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]

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