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65 lines
2.0 KiB
Bash
65 lines
2.0 KiB
Bash
#!/bin/bash
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## Last updated on Jan 9th 2024 by Auden Cote-L'Heureux
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#Intent: Calculate TPM for assembled transcripts
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#Dependencies: None
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#Inputs: Must be in a folder along with a folder called 'Transcriptomes', containing assembled transcripts as output by rnaSpades (transcripts.fasta),
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## and a folder called 'RawReads' containing the fwd and rev reads prior to assembly, with the same file prefixes as the corresponding assembled transcript files
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#Outputs: A folder, containing a 'quant' file which has TPM data.
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## If running on an HPC, include parameters here! For example, on a Slurm system you might use
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#SBATCH --job-name=tpm
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#SBATCH --output=Salmon.%j.out # Stdout (%j expands to jobId)
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#SBATCH --nodes=1
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#SBATCH --ntasks=60
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#SBATCH --mem=60G
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mkdir Indices
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## First, build transcript indices
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cd Transcriptomes
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IFS='/'
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for TRANS in *; do
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#read -a trapsplit <<<"$TRANS"
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#traf=${trapsplit[1]}
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tax=${TRANS:0:10}
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./../salmon-1.9.0_linux_x86_64/bin/salmon index -t $TRANS -i ../Indices/$tax
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done
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## Now calculate TPM
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cd Indices
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IFS='/'
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for TRANS in *; do
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read -a trapsplit <<<"$TRANS"
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tax=${TRANS:0:10}
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fpe='NA'; rpe='NA'; fpesub="FPE"; rpesub="RPE"
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for TRIM in ../RawReads/*; do
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read -a tripsplit <<<"$TRIM"
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trif=${tripsplit[2]}
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if [ "${trif:0:10}" == "$tax" ]; then
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if [[ "$trif" == *"$fpesub"* ]]; then
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fpe=$trif
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fi
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if [[ "$trif" == *"$rpesub"* ]]; then
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rpe=$trif
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fi
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fi
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done
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if [ "$rpe" != 'NA' ]; then
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./../salmon-1.9.0_linux_x86_64/bin/salmon quant -i $TRANS -l A -1 ../RawReads/$fpe -2 ../RawReads/$rpe --validateMappings -o ../quants/$tax
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fi
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if [ "$rpe" == 'NA' ]; then
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./../salmon-1.9.0_linux_x86_64/bin/salmon quant -i $TRANS -l A -r ../RawReads/$fpe --validateMappings -o ../quants/$tax
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fi
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done |