Skip to main content
Revision c5b88eb5aa3fa9f6a657d8b078405ce82f7e0e2d authored by Eric Sanford on 09 October 2019, 20:53:45 UTC, committed by Eric Sanford on 09 October 2019, 20:53:45 UTC
Updated STAR version, set default reference genome to hg38, added gene_names from gtf file when there is no HGNC symbol match, made it easier to change the reference genome by defining it in the setEnvironmentVariables.sh script. Modified some snakemake files to make that alternate pipeline almost runnable on the cluster in an interactive node.
1 parent e650685
Raw File Download
submitUnzipAndCat.sh 
#!/bin/bash

# The first input is the location of the raw data - this should be the location of your data.
# The second/final input is the destination - this should be your experiment folder.

$codeHomeDir/rajlabseqtools/Utilities/stepOneSetUp/unzipAndConcatenateZippedFastq.sh $RAWDATA_DIRECTORY /project/arjunrajlab/$PROJECT/repo/$EXPERIMENT $PAIRED_OR_SINGLE_END_FRAGMENTS