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This program is designed to do NGS data analysis with minimal options.
Description:
usage: QA2RNA-Seq.py [-h] [--seqType SEQTYPE] [--protocal PROTOCAL] [--infile INFILE [INFILE ...]] [--barcode BARCODE] [--barcodefile BARCODEFILE] [--adapter ADAPTER] [--adapterfile ADAPTERFILE] [--qualityscore QUALITYSCORE] [--mismatch MISMATCH] [--aligner ALIGNER] [--aligner-path ALIGNER_PATH] [--genome GENOME] [--transcriptome TRANSCRIPTOME] [--index INDEX] [--gfffile GFFFILE] [--gtffile GTFFILE] [--precursor PRECURSOR] [--mature MATURE] [--quantification QUANTIFICATION] [--processor PROCESSOR]
optional arguments: -h, --help show this help message and exit --seqType SEQTYPE, -sT SEQTYPE Select read sequence protocal either RNA-Seq or smallRNA-seq or WGS/Bisulfite/ChIP-Seq/CLIP/CLASH --protocal PROTOCAL, -p PROTOCAL Select read type either Single end (SE) or Paired end (PE) --infile INFILE [INFILE ...], -f INFILE [INFILE ...] Examples: -f file1.fq file2.fq --barcode BARCODE, -b BARCODE Barcode generated data answer in Yes/No --barcodefile BARCODEFILE, -bf BARCODEFILE Provide barcode file in fasta format --adapter ADAPTER, -ad ADAPTER Provide adapter sequence according to protocol in fasta format --adapterfile ADAPTERFILE, -adf ADAPTERFILE Provide adapter sequences file according to protocol --qualityscore QUALITYSCORE, -QS QUALITYSCORE Quality score for read filtering --mismatch MISMATCH, -ms MISMATCH Mismatch in adapter alignment --aligner ALIGNER, -al ALIGNER Alignment program Tophat2/Hisat2/Bowtie2/BWA --aligner-path ALIGNER_PATH, -alpath ALIGNER_PATH Please provide the executable path of Tophat2/Hisat2/Bowtie2/BWA --genome GENOME, -g GENOME Reference genome file --transcriptome TRANSCRIPTOME, -ts TRANSCRIPTOME Reference transcriptome file for RSEM expression analysis --index INDEX, -id INDEX Genome index name. Tophat2/bowtie2 takes bowtie2 index while others generated using their program /Hisat2/Bowtie2/BWA --gfffile GFFFILE, -gff GFFFILE Reference genome annotation file GFF3 --gtffile GTFFILE, -gtf GTFFILE Reference genome GTF file --precursor PRECURSOR, -prec PRECURSOR Precursor miRNA sequence file in fasta format --mature MATURE, -mat MATURE mature miRNA sequence file in fasta format --quantification QUANTIFICATION, -qt QUANTIFICATION Quantification/assembly by Cufflink/HTseq count utility/RSEM expression calculation --processor PROCESSOR, -n PROCESSOR Number of processor
Example 1: for RNA-Seq expression calculation
python3 QA2RNA-Seq.py -sT RNA -QS 30 --infile N2-1_CGATGT_L002_R1_001.fastq uY38-1_GCCAAT_L002_R1_001.fastq -ms 3 -n 20 -adf Current-Adapters.fa -al Hisat2 -g /media/ganesh/RA1/KSU/WormBase/w269/ensembl/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa -gtf /media/ganesh/RA1/KSU/WormBase/w269/ensembl/Caenorhabditis_elegans.WBcel235.95.gtf -gff /media/ganesh/RA1/KSU/WormBase/w269/ensembl/Caenorhabditis_elegans.WBcel235.95.gff3 -qt cufflink
Example 2: for small RNA-Seq based miRNA quantification
python3 QA2RNA-Seq.py -sT smallRNA --infile 7-N2-r2_S37_R1_001.fastq 9-84-r2_S38_R1_001.fastq -n 20 --barcodefile barcode_ip.fa --adapterfile smRNA-adp.fa --mismatch 3 -QS 25 --genome /media/ganesh/RA1/KSU/WormBase/w269/ensembl/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa --precursor /media/ganesh/RA1/KSU/WormBase/w269/ensembl/cel_precursor-DNA.fa --mature /media/ganesh/RA1/KSU/WormBase/w269/ensembl/cel_mature-DNA.fa