Question: Variant mapping workflow and tutorial in Galaxy
1
gravatar for Joachim.Berger
3 months ago by
Joachim.Berger40 wrote:

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...

ADD COMMENTlink modified 3 months ago • written 3 months ago by Joachim.Berger40
2
gravatar for Joachim.Berger
3 months ago by
Joachim.Berger40 wrote:

Anyone interested in mapping, check out the link in this post https://biostar.usegalaxy.org/p/26130/ Cheers, Joe

ADD COMMENTlink modified 3 months ago • written 3 months ago by Joachim.Berger40

Thanks! I missed that the author posted back about the new tools already :)

ADD REPLYlink written 3 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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 fastqsanger or 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

ADD COMMENTlink modified 3 months ago • written 3 months ago by Jennifer Hillman Jackson25k
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