hi all, trying to run tophat2 , with -G xx.gtf and bowtie2index. the command is :
tophat2 --library-type fr-unstranded -g 1 -G /home/..../**Homo_sapiens.GRCh38.90.gtf** /home/..../Homo_sapiens/UCSC/hg38/Sequence/**Bowtie2Index/genome** /home/.../xx.fastq
The error :
Building Bowtie index from Homo_sapiens.GRCh38.90.fa [FAILED] Error: Couldn't build bowtie index with err = 1
Same command was used for mouse and it worked. Also changed the gtf file and placed it into the same folder as the bowtie2index and it didnt work ( as i read a suggestion here )
edit: why is it trying to create Bowtie2index from the gtf file while i specified the index file!!