RNA-seq~HISAT2-StringTie-DEGanalysis

input_1:paired-end FASTQ(.gz) files

input_1/SRR1363434_1.fastq.gz

input_1/SRR1363434_2.fastq.gz

input_1/SRR1363435_1.fastq.gz

input_1/SRR1363435_2.fastq.gz

input_2:reference genome file

input_2/ref.fasta

>chrI
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA
CATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTT
ACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAAC
CACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATC
CAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATAC
TGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACACACACGTGCT
TACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTT
TACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTC
CACTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATG

input_3:reference gene model file (gtf or gff3) [optional]

input_3/saccharomyces_cerevisiae_R64-2-1_20150113.gff

##gff-version 3
#date Tue Jan 13 13:06:13 2015
#
# Saccharomyces cerevisiae S288C genome (version=R64-2-1)
#
# Features from the 16 nuclear chromosomes labeled chrI to chrXIV,
# plus the mitochondrial genome labeled chrmt.
#
# Created by Saccharomyces Genome Database (http://www.yeastgenome.org/)
#

input_4:sample information file [optional]

input_4/sample.input2.txt

id	condition
SRR1363434_1.fastq	Sc
SRR1363435_1.fastq	Sc
SRR1363436_1.fastq	Sc
SRR1363437_1.fastq	Sp
SRR1363438_1.fastq	Sp
SRR1363439_1.fastq	Sp

Output

0_result.html