Hi, I have a zebrafish mutant that I am trying to map. So I did the mapping crosses and sequenced the sibling and the homozygous pools, resulting in four sequence files: sib_R1.fastq.gz, sib_R2.fastq.gz, homo_R1.fastq.gz, and homo_R2.fastq.gz. How can I now do the mapping? I run into multiple issues with Galaxy: - I uploaded my files, but somehow the .gz files got unpacked and I am now over the allowed disk space. - For running "CloudMap Hawaiian Variant Mapping with WGS and Variant Calling workflow (no candidate genes)", I need a vcf file? - Trying to run the workflow "making a VCF file", but which files do I have to use for each input dataset? - What is this vcf file? - Is there a possibility to upload screen shots. Those are just a few problems that I am running into with Galaxy. Can someone point me in the right direction? I can't find suitable documentations...
The Cloudmap workflow has been deprecated. Replacement tools were in progress but I do not know the current status. Or you can check with the original tool authors, contact details are in this prior post: https://biostar.usegalaxy.org/p/22615/. I am trying to get an updated status but that might take some time.
This is the link to the original Cloudmap workflow/publication with usage help. Please be aware that not all of the tools will function as they did originally and may fail for odd reasons. If you are working at https://usegalaxy.org and one of these tools fail, there is no need to send in a bug report. https://usegalaxy.org/u/gm2123/p/cloudmap
For the upload issue, if the datatype is not set during upload compressed
fastq.gz files will be uncompressed and assigned to
fastq depending on whether Galaxy can detect
fastqsanger quality scores or not. To keep the data compressed, assign the datatype yourself within the upload tool. If you are certain that the data is in
fastqsanger format, then the datatype assignment can be set to
fastqsanger.gz (what most tools will require as input). FAQs: https://galaxyproject.org/support/#getting-inputs-right
Thanks! Jen, Galaxy team