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User: arup

gravatar for arup
arup • 820
Reputation:
820
Status:
Trusted
Location:
India
Website:
http://arupgsh.github.io/
Twitter:
arupgsh
Scholar ID:
Google Scholar Page
Last seen:
11 hours ago
Joined:
3 years, 2 months ago
Email:
a*******@gmail.com

PhD student @ Institute of Life Science, Bhubaneswar

Posts by arup

<prev • 136 results • page 1 of 14 • next >
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Answer: C: Can i use bwa aln to align my illumina sequence whose length is 150 bp?
... According to BWA [documentation][1], you can go up to 1Mbp with BWA MEM. > It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. > The first algorithm is designed for Illumina sequence reads up to > 100bp, while the rest two for longer sequences ranged from 70bp to > 1Mbp. ...
written 2 days ago by arup • 820
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Comment: C: Freelance bioinformatics jobs
... Join Kolabtree or Upwork for freelance jobs. ...
written 7 days ago by arup • 820
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Comment: C: Visualizing CNV data based from bed or bedgraph format
... Have you checked [aCNViewer][1] tool? [1]: https://github.com/FJD-CEPH/aCNViewer ...
written 10 days ago by arup • 820
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Comment: C: bcftools query missense_variant SNPs from gnomad VCF files
... Can you share the header and first few lines of the file? ...
written 16 days ago by arup • 820
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Answer: A: Python3: How to split the tuple generated by the .groupby function in pandas
... Any particular reason to keep tabs? import pandas as pd data = pd.read_csv("file.txt", header = None, delimiter="\t", names = ['chr', 'sTSS', 'eTSS', 'gene', 'clust1', 'clust2']) dup_clust2 = data.groupby('clust2').filter(lambda x: len(x) > 1).to_records().tolist() for t in dup_c ...
written 23 days ago by arup • 820
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Answer: A: Bulk download of entire BioProject SRA
... Download the [RunInfo][1] table and use parallel to download multiple files at once. #!/bin/bash #change the number after -j change the number of files to be processed. parallel --verbose -j 20 prefetch {} ::: $(cut -f5 SraRunTable.txt ) >>sra_download.log wait parallel - ...
written 23 days ago by arup • 820
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Answer: A: Loop over .sai files coupled with .fastq.gz
... If your system supports parallel the try the following command with some modifications in the file name pattern. parallel --verbose -j 20 'bwa mem -t 10 bwa_index {1}_1.fastq.gz {1}_2.fastq.gz|samtools sort -@5 -o {1}_sorted.bam -' ::: $(cat files.txt) Change the number after `-j` to increase ...
written 24 days ago by arup • 820
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Comment: C: R packages for Data mining or machine learning of a set of differentialy express
... Start with a [pathway enrichment analysis][1]. [1]: https://bioconductor.org/help/search/index.html?q=pathway/ ...
written 24 days ago by arup • 820
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Answer: A: snpEff building new database ERROR
... Prebuilt *Zea mays* database is already available, not sure about the version. java -jar /Toolbox/snpEff/snpEff.jar databases |grep "Zea" java -jar /Toolbox/snpEff/snpEff.jar download -v Zea_mays ...
written 24 days ago by arup • 820
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Comment: C: Help convert GDC exploration url to API download?
... Check the GDC API documentation. https://gdc.cancer.gov/developers/gdc-application-programming-interface-api ...
written 24 days ago by arup • 820

Latest awards to arup

Scholar 23 days ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 23 days ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Scholar 10 weeks ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Good Answer 3 months 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 3 months ago, created 100 posts.
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to use Biopython for fetching metadata of NCBI/GenBank/RefSeq assembly ident
Scholar 3 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Voter 4 months ago, voted more than 100 times.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 7 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 12 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Supporter 12 months ago, voted at least 25 times.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
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