Tophat

Tophat

build a index

bowtie2-build seaGenome.fna seaGenome.fna

##run tophat2

tophat2 -p 8 -i 20 -I 4000 --min-segment-intron 20 --max-segment-intron 4000 --min-coverage-intron 20 --max-coverage-intron 4000 --coverage-search --microexon-search -G Apostichopus_japonicus.gff --library-type fr-firststrand seaGenome.fna SRR771602.fastq

~/Biosoft/cufflinks-2.2.1.Linux_x86_64/cufflinks -p 8 -b ../tophat/erecta.fna -u -o sample1 ../tophat/tophat_out/accepted_hits.bam

merge the transcripts.gtf

cuffmerge -o merged_asm -p 8 -s ../../tophat/erecta.fna list