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nellore
Scalable RNA-seq analysis
I am running locally and installed via the installation command at http://rail.bio. I ran with the following command: rail-rna go local -x /path/Homo_sapiens/UCSC/hg38/Sequence/BowtieIndex/genome /path/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/genome -m run.manifest -o railrna -d tsv,bw,jx...
I run successfully the prep step with my 20 samples (1-2Gb each) When I run the align step in local mode rail-rna align local \ --gzip-intermediates --gzip-level 9 \ -x...
to include this commit: https://github.com/nellore/rail/commit/88dfa92d38aa7bfa0a18d0be060fc15dfc3bcf15 when you get a chance, thanks
Currently the prep_merge.R and prep_sample.R are a laborious second step. I would love to have the rse_exon.Rdata and rse_gene.Rdata ect, provided at the end of the rail run.
In the coverage_bigwigs hundreds of bw chromosome files are generated, provide an option to report only final bw file.
Since people may do multiple large, expensive runs with Rail, like we do, it's nice to be able to tag the EMR cluster so that the various projects can be...
Scenario: I have a bucket `blah` and my EMR job is set to output to a subdirectory of `blah`. When I try to run Rail starting from json: ``` cat...
This might be a problem with just my machine, but I just did a fresh install of Ubuntu onto a new SSD so it's possible others are experiencing this as...
make it obvious which log file has the error when dooplicity fails on a step in local/parallel modes
In local mode, L1750 of `emr_simulator.py` creates a temporary directory in `/tmp` when it should do this in the scratch directory specified by the user