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In order to use the bedtools command on our data, do the following:
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| Submit to the TACC queue or run in an idev shell | Submit to the TACC queue or run in an idev shelltitle | Warning: To submit to queue |
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nano commands.bedtools
bedtools multicov -bams C1_R1_thout/accepted_hits.bam C1_R2_thout/accepted_hits.bam C1_R3_thout/accepted_hits.bam C2_R1_thout/accepted_hits.bam C2_R2_thout/accepted_hits.bam C2_R3_thout/accepted_hits.bam -bed reference/genes.formatted.gtf > gene_counts.gff &
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launcher_creator.py -j commands.bedtools -n multicov -q normal -t 02:00:00 -a CCBB -l bedtools_launcher.sge
qsub bedtools_launcher.sge |
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| title | HTseq module on Lonestar is slightly broken |
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export PYTHONPATH=/opt/apps/htseq/0.5.4p5/lib/python2.7/site-packages/HTSeq-0.5.4p5-py2.7-linux-x86_64.egg/:$PYTHONPATH
module load htseq
$TACC_HTSEQ_DIR/scripts/htseq-count
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| title | Let's just take a look at the commands |
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$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > count1.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > count2.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > count3.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > count4.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > count5.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > count6.gff
join count1.gff count2.gff| join - count3.gff | join - count4.gff |join - count5.gff|join - count6.gff > gene_counts_HTseq.gff #if you have many samples, use for-loop and join |
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| Submit to the TACC queue or run in an idev shell | Submit to the TACC queue or run in an idev shelltitle | Warning: To submit to queue |
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nano commands.htseq
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > count1.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > count2.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C1_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > count3.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R1_thout/accepted_hits.sam reference/genes.formatted.gtf > count4.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R2_thout/accepted_hits.sam reference/genes.formatted.gtf > count5.gff
$TACC_HTSEQ_DIR/scripts/htseq-count -m intersection-nonempty -i gene_id C2_R3_thout/accepted_hits.sam reference/genes.formatted.gtf > count6.gff
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launcher_creator.py -j commands.htseq -n htseq -q normal -t 02:00:00 -a CCBB -l htseq_launcher.sge
qsub htseq_launcher.sge |
AFTER THIS COMPLETES: | Code Block |
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join count1.gff count2.gff| join - count3.gff | join - count4.gff |join - count5.gff|join - count6.gff > gene_counts_HTseq.gff
#if you have many samples, use for-loop and join |
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