User: arup

gravatar for arup
arup720
Reputation:
720
Status:
Trusted
Location:
India
Website:
http://arupgsh.github.io/
Twitter:
arupgsh
Scholar ID:
Google Scholar Page
Last seen:
2 days, 2 hours ago
Joined:
3 years ago
Email:
a*******@gmail.com

PhD student @ Institute of Life Science, Bhubaneswar

Posts by arup

<prev • 122 results • page 1 of 13 • next >
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... Are you sure its "multiple ensemble ids for a gene symbol" or "multiple gene symbols for an ensemble id"? ...
written 12 days ago by arup720
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Comment: C: Link for pre-indexed BWA indices for human reference
... I've uploaded the contents of README.txt in github. > Sequence/BWAIndex/ contains an index of the whole genome for use with > the BWA aligner. Since the BWA index scheme changed at version 0.6.0, > both versions 0.5.x and 0.6.0 (and higher) are included. https://gist.github.com/arupgsh/a8 ...
written 14 days ago by arup720
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Answer: A: Link for pre-indexed BWA indices for human reference
... Illumina has a collection of "Ready-To-Use" reference sequences for commonly studied organisms which include the fasta reference sequence, Bowtie2 index, and BWA index files. FIles: http://sapac.support.illumina.com/sequencing/sequencing_software/igenome.html?langsel=/in/ Documentation: ftp://uss ...
written 14 days ago by arup720
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Comment: C: p53 cancer patient RNA seq and protein sequence data
... To access TCGA data visit the [GDC][1] portal or access processed data using the [Firebrowse API][2].TP53 protein information can be found at [UniProt][3]. [1]: https://portal.gdc.cancer.gov/ [2]: http://firebrowse.org/api-docs/ [3]: https://www.uniprot.org/uniprot/P04637#sequences ...
written 15 days ago by arup720
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Comment: C: Feature extraction from DNA sequence
... The following article will give you an idea. https://www.nature.com/articles/s41588-018-0160-6 ...
written 15 days ago by arup720
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Comment: C: Error in bcftools view -bvcg command
... Hi, have you checked the sorted bam file? The command you mentioned for sorting is not correct. You can either redirect the ouput using `>` or can use the `-o` option. Also index the refernece fasta file with samtools in the same directory. samtools sort my.bam > my-sorted.bam samtoo ...
written 16 days ago by arup720
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Comment: C: Feature extraction from DNA sequence
... You want to check the association b/w variants and expression profile of the adjacent gene or going for expression prediction based on genotype? https://www.um.edu.mt/__data/assets/pdf_file/0005/289427/eQTL_intro.pdf ...
written 16 days ago by arup720
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Comment: C: Error in bcftools view -bvcg command
... Have you tried running them separately?? bcftools mpileup --redo-BAQ --min-BQ 30 --per-sample-mF --targets DP,AD -f ref.fasta input.sorted.bam | bcftools call --multiallelic-caller --variants-only >out.vcf set the `--ploidy ` if required in the variant calling step. ...
written 16 days ago by arup720
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Comment: C: common CNVs among multiple files
... Parse the chr and start end form CNVnator results then overlap the output file using `Bedtools multiIntersectBed` or `Bedops`. ...
written 18 days ago by arup720
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Comment: C: how to read .xlsx files perfectly into R using openxlsx package?
... Put the three tables in three different sheets and import them separately and remove the extra text form your excel file like "Data I have", "but I am getting like this". ...
written 23 days ago by arup720

Latest awards to arup

Scholar 14 days ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
Centurion 7 weeks ago, created 100 posts.
Scholar 7 weeks ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Voter 10 weeks ago, voted more than 100 times.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 5 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 10 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Supporter 10 months ago, voted at least 25 times.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]

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