I am trying to find UCEs in some earthworm genomes. To do so, I am working on the Tutorial IV from phyluce, and I am currently at the step "Align baits against exemplar genomes" using the command phyluce_probe_run_multiple_lastzs_sqlite.
I do not encounter an error message, however, some of the output files produced are empty. And it seems that those empty files correspond to the genomes that I did not download from NCBI.
I encountered a problem in a previous step (when I was running the phyluce_probe_get_tiled_probes) because of the format of the base genome headers (genome not from NCBI). So I modified headers of genomes that do not come from NCBI.
It seems that everything was working until the step "Align baits against exemplar genomes". I guess that my problem come from the 2bit files (and so from the original fasta file).
Can you give me some information about the format of the genome file when it is not download from NCBI? How to present it in order to follow the tutorial?
Thank you very much in advance for your help.
Marie
Hello,
I am trying to find UCEs in some earthworm genomes. To do so, I am working on the Tutorial IV from phyluce, and I am currently at the step "Align baits against exemplar genomes" using the command phyluce_probe_run_multiple_lastzs_sqlite. I do not encounter an error message, however, some of the output files produced are empty. And it seems that those empty files correspond to the genomes that I did not download from NCBI. I encountered a problem in a previous step (when I was running the phyluce_probe_get_tiled_probes) because of the format of the base genome headers (genome not from NCBI). So I modified headers of genomes that do not come from NCBI. It seems that everything was working until the step "Align baits against exemplar genomes". I guess that my problem come from the 2bit files (and so from the original fasta file). Can you give me some information about the format of the genome file when it is not download from NCBI? How to present it in order to follow the tutorial?
Thank you very much in advance for your help. Marie