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How to run R docker in WDL?

wdl R cromwell docker gatk written 7 months ago by c.clarido • 50

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730

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Bash vs WDL for running GATK

gatk cromwell pipeline linux wdl written 12 months ago by Mehulsharma.253 • 10 • updated 12 months ago by vdauwera • 960

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Recent Replies

C: No mutations or copy number alterations was detected in stage I of cancer by German.M.Demidov • 920
Check out this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5720395/ - it is not about alte...
A: replace gene names in gff file by Juke-34 • 3.1k
I would suggest to use agat_sp_manage_IDs.pl from [AGAT][1]. In same time it will standardize you...
C: No mutations or copy number alterations was detected in stage I of cancer by nazaninhoseinkhan • 390
Thank you so much for the explanation
C: No mutations or copy number alterations was detected in stage I of cancer by German.M.Demidov • 920
No mutations is indeed strange. Do you use panel sequencing? 1) tumor may be driven by epigeneti...
C: How to view gi_taxid_nucl.dmp that is 11.3 GB from NCBI by Ahill • 1.6k
On Windows, presuming the .dmp files are a delimited text format, you can view using the [more][1...
A: error in mat2csv ValueError: Shape of passed values is (4926, 33694), indices im by yueli7 • 80
should have a gene.tsv file
A: mat2csv IOError: Not a valid path to a feature-barcode mtx directory: '/home/li/ by yueli7 • 80
should have a gene.tsv file
C: How to view gi_taxid_nucl.dmp that is 11.3 GB from NCBI by peggyw • 0
sqlLite - interesting and not heard of grep. Windows is my primary tool, yes I know we are all ...
A: How to view gi_taxid_nucl.dmp that is 11.3 GB from NCBI by peggyw • 0
wrong place to post
C: How to view gi_taxid_nucl.dmp that is 11.3 GB from NCBI by Ahill • 1.6k
Google 'gi_taxid_nucl.dmp.gz' yields a 2013 article https://www.polarmicrobes.org/some-things-sho...
C: Correlation of two ChIP-seq signals? by biostart • 310
The code is quite standard, e.g. I calculated correlations between BigWig files using deepTools (...
A: How to Find Cell Type From Marker Genes (SC-RNA-Seq) by Kevin Blighe ♦ 52k
Apologies that nobody answered. Most researchers do indeed just use pre-compiled gene lists in or...

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