Hi,
I am new to the bioinformatics field but want to map my RNA-Seq data using TopHat. I've installed tophat and bowtie, however, when i run the programme, there is a error:
[Mon Jun 7 17:12:46 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 7 17:12:46 2010] Preparing output location ./tophat_out/
[Mon Jun 7 17:12:46 2010] Checking for Bowtie index files
[Mon Jun 7 17:12:46 2010] Checking for reference FASTA file
Warning: Could not find FASTA file rs4779584.fa
[Mon Jun 7 17:12:46 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Jun 7 17:12:46 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Mon Jun 7 17:12:46 2010] Checking reads
seed length: 36bp
format: fasta
[Mon Jun 7 17:14:48 2010] Mapping reads against rs4779584 with Bowtie
[Mon Jun 7 17:23:23 2010] Joining segment hits
[Mon Jun 7 17:24:24 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -6
I don't know what does "err= -6" mean
I have repeated many times and always meet the same mistake.
I am new to the bioinformatics field but want to map my RNA-Seq data using TopHat. I've installed tophat and bowtie, however, when i run the programme, there is a error:
[Mon Jun 7 17:12:46 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 7 17:12:46 2010] Preparing output location ./tophat_out/
[Mon Jun 7 17:12:46 2010] Checking for Bowtie index files
[Mon Jun 7 17:12:46 2010] Checking for reference FASTA file
Warning: Could not find FASTA file rs4779584.fa
[Mon Jun 7 17:12:46 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Jun 7 17:12:46 2010] Checking for Bowtie
Bowtie version: 0.12.5.0
[Mon Jun 7 17:12:46 2010] Checking reads
seed length: 36bp
format: fasta
[Mon Jun 7 17:14:48 2010] Mapping reads against rs4779584 with Bowtie
[Mon Jun 7 17:23:23 2010] Joining segment hits
[Mon Jun 7 17:24:24 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = -6
I don't know what does "err= -6" mean
I have repeated many times and always meet the same mistake.
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