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.
