{"push_id":629416398,"size":7,"distinct_size":7,"ref":"refs/heads/master","head":"bbc6f6d58649d5c45cd95c21f79b01471efdfd19","before":"074703f35c593aaeecf2955c37cc5efdabb037cf","commits":[{"sha":"17fd630c1799254e2205cc2b5dc3b18d6262e504","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Process reads using Snakemake. This probably won't be feasible. Having\nto run snakemake from a compute node and specify the correct working\ndirectory is really convoluted. Also, there is so much data, and having\nto add the extra memory needed by snakemake jobs is making the pipeline\nreally slow.","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/17fd630c1799254e2205cc2b5dc3b18d6262e504"},{"sha":"500596e94d4bf0c0d62b551d2df3f224a725e32d","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Download data from flow cell 02.","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/500596e94d4bf0c0d62b551d2df3f224a725e32d"},{"sha":"240c9c41998cee8215dbf73d0d6949ac44525a11","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Create submission script for sending large number of jobs to qsub. Also\ncreate script for trimming UMI's from reads. It is submitted as\nfollowed:\n\nsubmit.sh trim.sh 2g fastq/*fastq.gz","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/240c9c41998cee8215dbf73d0d6949ac44525a11"},{"sha":"99ec45aa899f49b1bf0ba0cb586129b991b33f1d","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Map reads with STAR. This strategy doesn't work well for the large\nnumber of files I have. While STAR does map reads very quickly (6\nminutes when loading genome; 2 minutes when genome pre-loaded), it\nrequires 32g of memory to run. Thus only 9 jobs run at a time. Even\nthough it is 5 times quicker than subread (i.e. 30 min per run), subread\ncan be run with 8g, thus 37 jobs at a time.","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/99ec45aa899f49b1bf0ba0cb586129b991b33f1d"},{"sha":"ca43a07240288c665c1cb7da9429bbdacd0211b5","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Revert to using subread for mapping intead of STAR.","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/ca43a07240288c665c1cb7da9429bbdacd0211b5"},{"sha":"17005782117c90021627628d7526a57cb8cf8c32","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Make create_genome executable.","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/17005782117c90021627628d7526a57cb8cf8c32"},{"sha":"bbc6f6d58649d5c45cd95c21f79b01471efdfd19","author":{"email":"5b232e11387ace3f316588355155f2f2e2929cc5@gmail.com","name":"John Blischak"},"message":"Ignore all hidden R files.","distinct":true,"url":"https://api.github.com/repos/jdblischak/singleCellSeq/commits/bbc6f6d58649d5c45cd95c21f79b01471efdfd19"}]}