Question: Tool does not recognise dataset as input
1
gravatar for EHC
4 months ago by
EHC10
EHC10 wrote:

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

ADD COMMENTlink modified 4 months ago • written 4 months ago by EHC10
0
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

The datatype for fastq datasets needs to be assigned to fastqsanger.

Three choices (updated):

  1. *Download the files from the Zenodo source. Then when upload to Galaxy, selecting the "fastqsanger" datatype.
  2. *Capture the URL. Then paste it into the Galaxy Upload tool, selecting the "fastqsanger" datatype.
  3. Change the datatype for datasets already loaded in Galaxy to have the 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

ADD COMMENTlink modified 4 months ago • written 4 months ago by Jennifer Hillman Jackson24k

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!

ADD REPLYlink written 4 months ago by EHC10
0
gravatar for EHC
4 months ago by
EHC10
EHC10 wrote:

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!

ADD COMMENTlink modified 4 months ago • written 4 months ago by EHC10
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