Question: Tophat Usage difficulty?
0
gravatar for jaqx008
8 months ago by
jaqx00870
jaqx00870 wrote:

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

ADD COMMENTlink modified 8 months ago • written 8 months ago by jaqx00870
1

Consider other alternative tools such as HISAT2 instead of Tophat.

<script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

ADD REPLYlink modified 8 months ago • written 8 months ago by Sej Modha4.7k

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

ADD REPLYlink written 8 months ago by jaqx00870
2
gravatar for 27atcggcta27
8 months ago by
27atcggcta27150
27atcggcta27150 wrote:

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.

ADD COMMENTlink written 8 months ago by 27atcggcta27150
0
gravatar for Mensur Dlakic
8 months ago by
Mensur Dlakic5.4k
USA
Mensur Dlakic5.4k wrote:

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

ADD COMMENTlink written 8 months ago by Mensur Dlakic5.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1720 users visited in the last hour