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Tophat Usage difficulty?

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

alignment tophat mapping bowtie2
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written by jaqx008 jaqx008

Consider other alternative tools such as HISAT2 instead of Tophat.

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written by Sej Modha Sej Modha

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

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written by jaqx008 jaqx008

2 answers

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.

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written by 27atcggcta27 27atcggcta27

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

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written by Mensur Dlakic Mensur Dlakic

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