Moderator: Arup Ghosh
Arup Ghosh ♦ 2.5k
- Reputation:
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- 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
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... 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 Ghosh ♦ 2.5k
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... 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 Ghosh ♦ 2.5k
2
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1
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41
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... Check the attached thread, https://www.biostars.org/p/334162/ . ...
written 7 hours ago by
Arup Ghosh ♦ 2.5k
0
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105
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1
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... 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 Ghosh ♦ 2.5k
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64
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... Check the methods section of FANTOM5 article.
https://www.nature.com/articles/nature12787 ...
written 15 days ago by
Arup Ghosh ♦ 2.5k
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63
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... Please share the command you are using. ...
written 15 days ago by
Arup Ghosh ♦ 2.5k
1
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1
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59
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1
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... 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 Ghosh ♦ 2.5k
0
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1
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82
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1
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... Kegg pathways can be manipulated using [PathVisio][1].
[1]: https://pathvisio.github.io/ ...
written 17 days ago by
Arup Ghosh ♦ 2.5k
1
vote
1
answer
82
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1
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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 Ghosh ♦ 2.5k
0
votes
1
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88
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1
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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 Ghosh ♦ 2.5k
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