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2

Python dictionaries are indeed a good tool for that. Here is a script that takes 2 arguments (the file containing the counts and the file containing the genome length info), and prints the input data, with an added column containing coverage: #!/usr/bin/env python3 import sys counts_fname = sys.argv[1] genome_lengths_fname = sys.argv[2] ...


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I would do it in R: tab1 <- read.table('file1.tsv', header = T, stringsAsFactors = F) tab2 <- read.table('file2.tsv', header = T, stringsAsFactors = F) merged_tav <- merge(reads_tab, genome_len_tab) merged_tav$z <- merged_tav$x / merged_tav$y merged_tav returns ID Info Info2 x y z 1 E81292 info info 10200 13101 0....


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Assuming your user is in the group permitted to use docker: docker pull quay.io/biocontainers/tophat:2.1.1--py27_3 nohup docker run -v /some/path:/data quay.io/biocontainers/tophat:2.1.1--py27_3 tophat2 ... & The only thing to remember is to mount everything you'll need into the docker container (/data in the example above). If you need to debug things ...


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