Tophat Usage difficulty?

Question

[jaqx008]

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

Error message

[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

[Sej Modha]

Consider other alternative tools such as HISAT2 instead of Tophat.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in 2008. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

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[jaqx008]

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

Answer 1

[27atcggcta27]

here is a link to the manual for tophat TOPHAT2 MANUAL

I highly suggest you use hisat2 over tophat though. It is a much better option.

Answer 2

[Mensur Dlakic]

See if making the output directory (and tmp directory within it) changes your luck. Do this in a directory where your .fasta file is.

mkdir -p tophat_out/tmp