Question: Problem with running tophat2
0
gravatar for Genosis
21 months ago by
Genosis20
Genosis20 wrote:

Hello everyone,

this is the first time i'm trying to run tophat2 on a computer cluster, which already has tophat2 / cufflinks and GTF files pre-installed. I am pretty new to the UNIX environment so I apologise if this question seems too 'basic'.

For my experiment: My fastq files are human, paired end reads from illumina. First step I'm trying to align the reads to the reference genome with tophat 2.

The command which I was told to use was: (From Trapnell's protocol)

tophat -p 8 --gtf /gpfs/public/reference_genomes2/hg38/Homo_sapiens.GRCh38.84.gtf -o hg38 sample_read1.fastq.gz sample_read2.fastq.gz

This is the message that I got back: Traceback (most recent call last): File "/gpfs/public/tools/tophat-2.0.14.Linux_x86_64/tophat", line 4095, in <module> sys.exit(main()) File "/gpfs/public/tools/tophat-2.0.14.Linux_x86_64/tophat", line 3846, in main args = params.parse_options(argv) File "/gpfs/public/tools/tophat-2.0.14.Linux_x86_64/tophat", line 1033, in parse_options self.max_hits = int(value) ValueError: invalid literal for int() with base 10: 'tf'

And when I tried this tophat -p 8 -G /gpfs/public/reference_genomes2/hg38/Homo_sapiens.GRCh38.84.gtf -o hg38 sample_read1.fastq.gz sample_read2.fastq.gz

[2016-06-03 19:47:16] Beginning TopHat run (v2.0.14)

[2016-06-03 19:47:16] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-06-03 19:47:16] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (sample_read1.fastq.gz.*.bt2)

And this... $ tophat --GTF /gpfs/public/reference_genomes2/hg38/Homo_sapiens.GRCh38.84.gtf threads 1 --output-dir testoutput hg38C sample_read1.fastq.gz sample_read2.fastq.gz

[2016-06-03 19:44:43] Beginning TopHat run (v2.0.14)

[2016-06-03 19:44:43] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-06-03 19:44:44] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (threads.*.bt2)

So I created an index file and it's located in the same directory as the fastq files but it can't seem to recognise it and the error messages are driving me mad...

Thank you very much for your advice.

rna-seq tophat bowtie rnaseq • 664 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson24k • written 21 months ago by Genosis20
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Reference genome indexes need to be loaded, created, and referenced in a specific way when used with Galaxy wrapped tools. Try using the Data Managers in the Tool Shed to install them. http://usegalaxy.org/toolshed

After that, if you want to execute the tool on the command-line, first run the tool through the user interface to understand how the command-line should be constructed. This is reported on the "i" (info icon) Job Details report, per result dataset, found in the icons under the dataset's name.

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson24k
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