Moderator: Arup Ghosh

gravatar for Arup Ghosh
Arup Ghosh2.5k
Reputation:
2,460
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Location:
India
Website:
https://arup.dev/
Twitter:
arupgsh
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Google Scholar Page
Last seen:
2 hours ago
Joined:
4 years, 6 months ago
Email:
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PhD student @ Institute of Life Science, Bhubaneswar

Posts by Arup Ghosh

<prev • 317 results • page 1 of 32 • next >
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Comment: C: Error downloading streams from SRA-ncbi when running fastq-dump
... Try [Aspera secure copy][1]. [1]: https://www.ncbi.nlm.nih.gov/books/NBK158898/#SRA_download.when_should_i_use_aspera_co ...
written 7 hours ago by Arup Ghosh2.5k
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Answer: A: updating SNP names in VCF file
... dbSNP annotation can be added in the `ID` filed using the `VariantAnnotator` tool from GATK. gatk --java-options '-Xmx4G' \ VariantAnnotator \ -R /userdata/arup/hpcc_test/genome/hg38/hg38.fa \ -V input.vcf.gz \ -O output.vcf.gz \ --dbsnp dbsnp.vcf.gz ...
written 7 hours ago by Arup Ghosh2.5k
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Answer: C: Simple explanation and usage of WGCNA package?
... Check the attached thread, https://www.biostars.org/p/334162/ . ...
written 7 hours ago by Arup Ghosh2.5k
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Answer: A: Ensembl ID to ENTREZ best converter
... You can use `AnnotationDbi` to convert Ensembl ids. The code snippet converts Ensembl id to Entrez ids. library("AnnotationDbi") library("org.Hs.eg.db") #columns(org.Hs.eg.db) # returns list of available keytypes data$entrez = mapIds(org.Hs.eg.db, keys=row.na ...
written 9 hours ago by Arup Ghosh2.5k
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Comment: C: Finding enhancers of the whole human body
... Check the methods section of FANTOM5 article. https://www.nature.com/articles/nature12787 ...
written 15 days ago by Arup Ghosh2.5k
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Comment: C: SnpEff with files from 1001 genomes (sequences from Arabidopsis thaliana).
... Please share the command you are using. ...
written 15 days ago by Arup Ghosh2.5k
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Answer: C: Whole-genome human-mouse syntenic block tracks/database
... The following portal can generate synteny blocks for multiple species. http://bioinfo.konkuk.ac.kr/synteny_portal/htdocs/synteny_builder.php ...
written 15 days ago by Arup Ghosh2.5k
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Answer: C: Drawing KEGG-type metabolic pathways
... Kegg pathways can be manipulated using [PathVisio][1]. [1]: https://pathvisio.github.io/ ...
written 17 days ago by Arup Ghosh2.5k
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Answer: C: GATK 3.8 and GATK 3.7 scripts
... `GenomeAnalysisTK.jar` and `Picard.jar` were separate tools up to GATK v3.8. But from v4, Picard has been integrated into the Genome Analysis toolkit. GATK archive(< v3.8) : https://console.cloud.google.com/storage/browser/gatk-software/package-archive/gatk/ Picard stand-alone: https://broadin ...
written 22 days ago by Arup Ghosh2.5k
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Comment: C: Bowtie2 aligning output
... What's your primary goal, variant calling or (pairwise/multiple) sequence alignment? ...
written 22 days ago by Arup Ghosh2.5k

Latest awards to Arup Ghosh

Scholar 6 hours ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Scholar 6 hours ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Scholar 8 weeks ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
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]
Popular Question 3 months ago, created a question with more than 1,000 views. For Seurat vs Monocle
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Errors with SRA-toolkit: not enough space on the disk. (112)
Scholar 7 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Errors with SRA-toolkit: not enough space on the disk. (112)
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
Scholar 8 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Scholar 8 months ago, created an answer that has been accepted. For A: scatter plot in ggplot2 two colour for two different condition
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
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Good Answer 9 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
Scholar 9 months ago, created an answer that has been accepted. For A: How can I uninstall my packages in Rstudio
Teacher 9 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
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualising BedGraph files on UCSC [custom tracks]
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: scatter plot in ggplot2 two colour for two different condition

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