Hello All, I am having difficulty understanding and executing the tophat usage after looking up the help. its just not as simple as running other aligners like bowtie and I am needing help. below is the command I put together from what I understand. ( my reads are single end btw). can someone tell me what I am doing wrong and how the command is usually written so it execute without complain?
tophat --GTF Genome.Bw2.index.fa --library-type fr-unstranded --num-threads 24 Genome.Bw2.index Male.fastq --output-dir
[2019-10-02 10:46:19] Building transcriptome data files ./tophat_out/tmp/Genome.Bw2.index [2019-10-02 10:46:27] Building Bowtie index from Genome.Bw2.index.fa [FAILED] Error: Couldn't build bowtie index with err = 1
Consider other alternative tools such as HISAT2 instead of Tophat.
Thanks for your responses and suggestions. I figured the command works if the last imputes on the command include a reference genome index folled by the fastq RNAseq file. Again thank you