Hello, I am trying to built a very small demonstration for class.
I looking to show: paired fastq upload -> bwa or bowtie mapping ->igv. I checked a variety of teaching material.
I tried these two: https://zenodo.org/record/582600#.WczAmkojFhA https://zenodo.org/record/842795#.WczGGEojFhA but bwa-mem and bowtie2 can not recognize the files
I appreciate your help. Thanks ehc
Hello,
The datatype for fastq datasets needs to be assigned to fastqsanger.
Three choices (updated):
fastqsanger datatype. This is how: The tool I'm using does not recognize any input datasets. Why?*Choices 1 & 2 will change in the next release (version 17.09). An upgrade to the Upload tool will then load fastq data that meets fastqsanger format specifications with that datatype automatically assigned. 17.09 is active at Galaxy Main (https://usegalaxy.org) as of yesterday with an expected stable release date in about two weeks for local and docker Galaxy.
All Support FAQs: https://galaxyproject.org/support/
Hope that helps! Jen, Galaxy team
Thanks for the help. it worked (although I tried that before ..). However I do not manage to see the bam on igv. I have igv locally and open it first but it seems as empty if I use the local link or even if I download the galaxy bam/bam.bai and upload to igv independently. Thanks!