Commit 13fa2a11 authored by Davis McCarthy's avatar Davis McCarthy
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Adding readme

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# Melanoma-RegevGarraway-DFCI-scRNA-Seq
This project is a re-analysis of human melanoma single-cell RNA-seq and
corresponding whole-exome sequencing data from the Regev and Garraway groups at
the Broad Institute, Boston, USA.
......@@ -37,7 +37,8 @@ knownIndels100G = '/hps/nobackup/stegle/users/mjbonder/ref/GenotypingInformation
star_genome_files = ['chrLength.txt', 'chrNameLength.txt', 'chrName.txt', 'chrStart.txt', 'exonInfo.tab', 'Genome', 'genomeParameters.txt', 'SA', 'SAindex', 'sjdbInfo.txt', 'sjdbList.fromGTF.out.tab', 'sjdbList.out.tab', 'transcriptInfo.tab']
## define commands
salmon_idx = 'references/GRCh37/Homo_sapiens.GRCh37.rel75.cdna.all.ERCC92.salmon_v0.8.2_idx'
##salmon_idx = 'references/GRCh37/Homo_sapiens.GRCh37.rel75.cdna.all.ERCC92.salmon_v0.8.2_idx'
salmon_idx = 'references/GRCh37/Homo_sapiens.GRCh37.rel75.cdna.all.ERCC92.kmer.17.salmon_idex'
## parameter objects and samples
GENOME = 'genome.fa'
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