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Scripts for lncRNA Project is a novel mass spectrometry-based peptide sequencing pipeline of the identification of LncRNA-derived immunopeptidome.

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lncRNA_Scripts

Scripts for lncRNA Project

Synopsis

These are the scripts used to find the epitopes that bind to lncRNAs.

Scripts:

From Vikram Misra: These scripts are written in Bash shell script.

Pre-requisites: Need Bash shell, samtools and bedtools.

bed-intersect.sh - Finds intersection between two BED files.

Usage: bash bed-intersect.sh example.bed

bam_to_bed.sh - Converts BAM files to BED files.

Usage: bash bam_to_bed.sh example.bam

chrom-namer.sh - converts chromosome names from one format to another.

Usage: bash chrom-namer.sh example.bed

all-chrom.txt - two-column list of chromosome notations used by chrom-namer.sh

From Mohammad Haghir Ebrahimabadi: These scripts are in Python 2.

sample.py - For sampling mock lncRNA sequences from a genome.

Usage: python sample.py genome.fasta

pval.py - p-value calculation

All files with lncipedia_5_2_hc.fasta.aa.part-**.fasta names - Six-frame translations of the lncRNA sequences from https://lncipedia.org/

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Scripts for lncRNA Project is a novel mass spectrometry-based peptide sequencing pipeline of the identification of LncRNA-derived immunopeptidome.

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