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/