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dcc_commands.txt
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# dcc
# first paired end alignment
STAR --runThreadN 10 --genomeDir . --outSAMtype BAM SortedByCoordinate --readFilesIn HAL01_R1_trimmed.fastq HAL01_R2_trimmed.fastq --outFileNamePrefix halo1_r --outReadsUnmapped Fastx --outSJfilterOverhangMin 15 15 15 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 15 --outFilterMultimapNmax 20 --outFilterScoreMin 1 --outFilterMatchNmin 1 --outFilterMismatchNmax 2 --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15
# create sample dir
# first read alignment
STAR --runThreadN 10 --genomeDir ../ --outSAMtype None --readFilesIn ../HAL01_R1_trimmed.fastq --outFileNamePrefix halo1_r --outReadsUnmapped Fastx --outSJfilterOverhangMin 15 15 15 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 15 --seedSearchStartLmax 30 --outFilterMultimapNmax 20 --outFilterScoreMin 1 --outFilterMatchNmin 1 --outFilterMismatchNmax 2 --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15
# get out of there
cd ..
# make new mate_2 dir
mkdir mate_2
# alignment 3/media/daniel/NGS1/RNASeq/find_circ/circexplorer/CIRCexplorer/circexplorer1_starter_1.pl
STAR --runThreadN 10 --genomeDir ../ --outSAMtype None --readFilesIn ../HAL01_R2_trimmed.fastq --outFileNamePrefix halo1_r --outReadsUnmapped Fastx --outSJfilterOverhangMin 15 15 15 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 15 --seedSearchStartLmax 30 --outFilterMultimapNmax 20 --outFilterScoreMin 1 --outFilterMatchNmin 1 --outFilterMismatchNmax 2 --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15
# then
DCC sample1/halo1_rChimeric.out.junction -mt1 mate_1/halo1_rChimeric.out.junction -mt2 mate_2/halo1_rChimeric.out.junction -D -fg -an hg19_ens.gtf -Pi -M -Nr 1 1 -A hg19.fa -N -T 10 -an hg19_ref1.gtf
# run DCC
DCC sample1/halo1_rChimeric.out.junction -mt1 mate_1/halo1_rChimeric.out.junction -mt2 mate_2/halo1_rChimeric.out.junction -D -F -fg -an hg19_ens.gtf -Pi -M -Nr 1 1 -A hg19.fa -N -T 10-A hg19.fa