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IR.out.tab creation manual

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Woody Lin edited this page Apr 9, 2022 · 2 revisions

IR.out.tab for advanced users.

PSI-Sigma reads the .bam file and estimate the abundance of an intron based the read counts of 5 sampling points within the intron. It uses samtools to count and will take ~1 hour per sample. By default, PSI-Sigma will generate the IR.out.tab file sequentially (one by one), so it will take a long time to process. However, if the IR.out.tab files with correct prefix are already generated, PSI-Sigma will skip the step and directly use the IR.out.tab file already in the folder. This tutorial is meant to show how to generate IR.out.tab file in parallel (8GB RAM per thread).

Step 1: generate .db file.

Step 2: After the .db is generated, PSIsigma-ir-v.1.2.pl can be used to generate IR.out.tab file for each sample, respectively.

  • Note1: [database] is from step 1. Assuming PSIsigma1d9r.db is the name of the database.
  • Note2: [type] is equal to the --type parameter. Set to 1 for Illumina's short-read RNA-seq. Set to 2 for Nanopore's long-read RNA-seq data.
#PSIsigma-ir-v.1.2.pl [database] [.bam file] [type]
perl ~/PSI-Sigma-1.9r/PSIsigma-ir-v.1.2.pl PSIsigma1d9r.db WT1.Aligned.sortedByCoord.out.bam 1 &
perl ~/PSI-Sigma-1.9r/PSIsigma-ir-v.1.2.pl PSIsigma1d9r.db WT2.Aligned.sortedByCoord.out.bam 1 &
perl ~/PSI-Sigma-1.9r/PSIsigma-ir-v.1.2.pl PSIsigma1d9r.db WT3.Aligned.sortedByCoord.out.bam 1 &
perl ~/PSI-Sigma-1.9r/PSIsigma-ir-v.1.2.pl PSIsigma1d9r.db MT1.Aligned.sortedByCoord.out.bam 1 &
perl ~/PSI-Sigma-1.9r/PSIsigma-ir-v.1.2.pl PSIsigma1d9r.db MT2.Aligned.sortedByCoord.out.bam 1 &
perl ~/PSI-Sigma-1.9r/PSIsigma-ir-v.1.2.pl PSIsigma1d9r.db MT3.Aligned.sortedByCoord.out.bam 1 &
wait

Step 3: --name PSIsigma1d9r will make PSI-Sigma believe that PSIsigma1d9r.db has been generated.

perl ~/PSI-Sigma-1.9r/dummyai.pl --gtf Homo_sapiens.GRCh38.100.sorted.gtf --nread 10 --name PSIsigma1d9r --type 1 --fmode 3
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