diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh index b4cb8851ece1c99f502b735d7db9b11e560993db..ed85697bbd993c8c0586ceb213ee34b95dc9635e 100644 --- a/alignment/rnaseqalign.sh +++ b/alignment/rnaseqalign.sh @@ -50,6 +50,7 @@ then module load star/2.4.2a STAR --genomeDir ${index_path}/star_index/ --readFilesIn $fq1 $fq2 --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out else + module load star/2.4.2a STAR --genomeDir ${index_path}/star_index/ --readFilesIn $fq1 --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out fi mv outLog.final.out ${pair_id}.alignerout.txt