set up default reference files links and default params file

NYU-BFX · Jun 17, 2016 · 9463d19 · 9463d19
1 parent 9285404
commit 9463d19
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Showing 4 changed files with 5 additions and 2 deletions.
diff --git a/params b/params
@@ -1,5 +1,5 @@
-STAR-Genome	--genomeFastaFiles referenceFiles/genome.fa 
-fastq-download	meta_data
+#STAR-Genome	--genomeFastaFiles referenceFiles/genome.fa 
+#fastq-download	meta_data
 fastq-link	GTC
 #fastqc	meta_data/sra_info.txt
 STAR	--readFilesCommand zcat --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --genomeDir referenceFiles/STAR_Reference --sjdbGTFfile referenceFiles/gencode.v19.annotation.gtf

diff --git a/referenceFiles/STAR_Reference b/referenceFiles/STAR_Reference
@@ -0,0 +1 @@
+/ifs/home/gongy05/references/hg19/STAR_Reference/
diff --git a/referenceFiles/chromInfo.txt b/referenceFiles/chromInfo.txt
@@ -0,0 +1 @@
+/ifs/home/gongy05/references/hg19/chromInfo.txt
diff --git a/referenceFiles/gencode.v19.annotation.gtf b/referenceFiles/gencode.v19.annotation.gtf
@@ -0,0 +1 @@
+/ifs/home/gongy05/references/hg19/gencode.v19.annotation.gtf
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		/ifs/home/gongy05/references/hg19/STAR_Reference/
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		/ifs/home/gongy05/references/hg19/chromInfo.txt
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		/ifs/home/gongy05/references/hg19/gencode.v19.annotation.gtf