This repository is to cuantify RNA-seq data:
'/home/hawkins/Documents/Cesar/RNA/globus/lordec_reports/rna_seq/rna_seq_fastq'
Data used as reference:
genome1=/home/hawkins/Documents/Cesar/NGSEP/ngsep_tutorial/ZhongmuNo1/ZhongmuNo.1_genome.fasta
transc1=/home/hawkins/Documents/Cesar/NGSEP/ngsep_tutorial/ZhongmuNo1/ZhongmuNo.1.gff3
Data generated by iso-seq:
genome1='/home/hawkins/Documents/Cesar/NGSEP/ngsep_tutorial/ZhongmuNo1/ZhongmuNo.1_genome.fasta'
transc2='/home/hawkins/Documents/Cesar/RNA/globus/lordec_reports/lordec_trim/bed_Shen/ORF_NMD/blast_corrected_shen.bed'
transc3='/home/hawkins/Documents/Cesar/RNA/globus/lordec_reports/lordec_trim/bed_Shen/ORF_NMD/blast_corrected_shen.gtf'
transc4='/home/hawkins/Documents/Cesar/RNA/globus/lordec_reports/lordec_trim/bed_Shen/ORF_NMD/blast_corrected_shen.2.GFF3'
transc2 has 996554 lines
transc3 has 12970020 lines
transc4 has 9052682 lines
1_fastp.sh
This script make a quality control check similar to trimmomatic
2_salmon_quant.sh
This script will align and quantify your fastq files to obtain a file with tpm in quant.sf
3_mv_salmon.sh
This script moves all quant.sf files in a new directory to import them with tximport R package
tximport.R
This is the R script to import all quant.sf files. There are (at least) two options to identify DEG: Deseq2 and edgeR