Hi!
I am trying Velvet Optimiser vlsci with the contigs obtained with velvetg (from ion torrent raw data) and the resulting files appear in green, like 'everything went ok',but there are no files or data to show, when I click on the title, it says 'empty' , in the message chart appears 'no peek'. What am I doing wrong? Can anyone help me?. Thank you.
Lidia
Hello Lidia,
This problem can occur when the inputs to the tool are mismatched in some way. A common cause is that the chromosome identifiers are not an exact match. Check over the inputs to compare and see if that is the case, then adjust as needed for a first pass solution.
This wiki help mostly covers reference genome mismatch issues, but very similar advice can apply to nearly all inputs to tools (reference annotation, mapped fastq datasets, etc. - any data dependent on a common chromosome/contig). To extract the chromosome identifiers in a BAM/SAM dataset, use one of the index summary tools from the SAMTools or Picard tool group (if available on the server you are working on).
http://wiki.galaxyproject.org/Support#Reference_genomes
Thanks, Jen, Galaxy team
Sorry,I think I don't understand your answer. I am new doing 'de novo' assemblies. Do you mean read identifiers?, I am not using reference genomes. Or Velvet optimiser requires reference genomes?. Thank you for your help
