Closed hcdenbakker closed 8 years ago
Hi @hcdenbakker,
I think this is down to poor documentation - sorry!
sample_*fastq.gz should be the path to your fastq and the gn-amr-genes.fasta.gz should be a path to the file.
For example, if we're in the atlas dir something like this should work by replacing the fastq path to one of your fastq:
atlas genotype C00007012 mykatlas/data/gn-amr-genes.fasta.gz --seq /data2/users/phelim/data/gn/atlas/fastqs/C00007012.fastq.gz --mccortex31_path /home/henk/atlas/mccortex/bin/mccortex31
Thanks Phelim, Makes perfect sense, I am just trying to figure out what I can/can't do with atlas and it is probably a little bit premature to update the docs at this stage of development.
No problem @hcdenbakker. Let me know if you have any questions about what can be done. You can create your own panels for genotyping if required.
Tried my first atlas genotyping, tried the genotype gene panel example: atlas genotype :sample sample_*.fastq.gz gn-amr-genes.fasta.gz This did not work, gave me the following error: atlas: error: unrecognized arguments: sample_2.fastq.gz gn-amr-genes.fasta.gz
I ran into multiple errors, but in the end I got it to work with the following command line: atlas genotype --seq sample_*.fastq.gz --mccortex31_path /home/henk/atlas/mccortex/bin/mccortex31 sample gn-amr-genes.fasta.gz
Do the docs need updating, or is this something related to my system?