Commit 3ec24143 authored by Holger Brandl's avatar Holger Brandl

added workaround for network filesystem problems

parent eaf2dec9
......@@ -130,6 +130,7 @@ for (fastqFile in fastqFiles) {
val cmd = """
STAR --genomeDir ${star_index} --readFilesIn ${fastqFile} ${revReads} --runThreadN 6 ${optionalZcat} --outFileNamePrefix ${fastqBaseName}. --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --sjdbGTFfile ${gtfFile} --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --quantMode GeneCounts --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3
sleep 5 # to avoid filsystem issues on network volumnes
mv ${fastqBaseName}.Aligned.sortedByCoord.out.bam ${fastqBaseName}.bam
samtools index ${fastqBaseName}.bam
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment