RNA-seq~DEGanalysis

input_1:ballgown input (StringTie output)

input_1/SRR1363434_10k_1.fastq.stringtie.tar.gz

input_1/SRR1363435_10k_1.fastq.stringtie.tar.gz

input_1/SRR1363436_10k_1.fastq.stringtie.tar.gz

input_1/SRR1363437_10k_1.fastq.stringtie.tar.gz

input_1/SRR1363438_10k_1.fastq.stringtie.tar.gz

input_1/SRR1363439_10k_1.fastq.stringtie.tar.gz

input_2:Cuffdiff input (Cuffquant output)

input_2/SRR1363434_10k_1.fastq.cuffquant.tar.gz

input_2/SRR1363435_10k_1.fastq.cuffquant.tar.gz

input_2/SRR1363436_10k_1.fastq.cuffquant.tar.gz

input_2/SRR1363437_10k_1.fastq.cuffquant.tar.gz

input_2/SRR1363438_10k_1.fastq.cuffquant.tar.gz

input_2/SRR1363439_10k_1.fastq.cuffquant.tar.gz

input_3:sample information file

input_3/sample.txt

id	strain
SRR1363434_10k_1.fastq	a
SRR1363435_10k_1.fastq	a
SRR1363436_10k_1.fastq	a
SRR1363437_10k_1.fastq	b
SRR1363438_10k_1.fastq	b
SRR1363439_10k_1.fastq	b

input_4:reference genome file

input_4/ref.fasta

>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA
CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT
ACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAAC
CACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATC
CAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATAC
TGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACACACACGTGCT
TACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTC
CACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATG

input_5:reference gtf file

input_5/saccharomyces_cerevisiae_R64-2-1_20150113.gtf

chrmt	stdin	transcript	85554	85709	.	+	.	gene_id "Q0297"; transcript_id "Q0297_mRNA";  gene_name "Q0297";
chrmt	stdin	exon	85554	85709	.	+	.	gene_id "Q0297"; transcript_id "Q0297_mRNA"; exon_number "1"; exon_id "Q0297_mRNA.1"; gene_name "Q0297";
chrmt	stdin	CDS	85554	85706	.	+	0	gene_id "Q0297"; transcript_id "Q0297_mRNA"; exon_number "1"; exon_id "Q0297_mRNA.1"; gene_name "Q0297";
chrmt	stdin	start_codon	85554	85556	.	+	0	gene_id "Q0297"; transcript_id "Q0297_mRNA"; exon_number "1"; exon_id "Q0297_mRNA.1"; gene_name "Q0297";
chrmt	stdin	stop_codon	85707	85709	.	+	0	gene_id "Q0297"; transcript_id "Q0297_mRNA"; exon_number "1"; exon_id "Q0297_mRNA.1"; gene_name "Q0297";
chrmt	stdin	transcript	79213	80022	.	+	.	gene_id "Q0275"; transcript_id "Q0275_mRNA";  gene_name "Q0275";
chrmt	stdin	exon	79213	80022	.	+	.	gene_id "Q0275"; transcript_id "Q0275_mRNA"; exon_number "1"; exon_id "Q0275_mRNA.1"; gene_name "Q0275";
chrmt	stdin	CDS	79213	80019	.	+	0	gene_id "Q0275"; transcript_id "Q0275_mRNA"; exon_number "1"; exon_id "Q0275_mRNA.1"; gene_name "Q0275";
chrmt	stdin	start_codon	79213	79215	.	+	0	gene_id "Q0275"; transcript_id "Q0275_mRNA"; exon_number "1"; exon_id "Q0275_mRNA.1"; gene_name "Q0275";
chrmt	stdin	stop_codon	80020	80022	.	+	0	gene_id "Q0275"; transcript_id "Q0275_mRNA"; exon_number "1"; exon_id "Q0275_mRNA.1"; gene_name "Q0275";

input_6:Trinotate output file

input_7:Trinotate.xls3.isoform.cnt

input_8:Trinotate.xls3.gene.cnt

input_9:Trinotate.xls3.go.cnt

Command

Output

0_result.html

Log

pp RNA-seq~DEGanalysis -c 8 -m 32 input_1/ input_2/ input_3/sample.txt input_4/ref.fasta input_5/saccharomyces_cerevisiae_R64-2-1_20150113.gtf