Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • ngsclialab/process_scripts
  • astrocyte/workflows/bicf/process_scripts
Show changes
Commits on Source (1)
Hide whitespace changes
Inline Side-by-side
alignment/rnaseqalign.sh
View file @ 0bdf56d5
......@@ -45,7 +45,7 @@ diff $fq1 $fq2 > difffile.out
if [ $algo == 'star' ]
then
if (-s difffile)
if [ -s difffile ]
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
......@@ -54,7 +54,7 @@ then
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
mv outAligned.sortedByCoord.out.bam output.bam
mv outAligned.sortedByCoord.out.bam ${pair_id}.bam
else
module load hisat2/2.1.0-intel
if [ -s difffile ]
......@@ -69,8 +69,8 @@ else
else
samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
fi
samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -n -o output.nsort.bam output.bam
java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
fi
samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -n -o output.nsort.bam output.bam
java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam