Question: Cannot find files - Bowtie2 or Tophat
gravatar for yena.oh
13 months ago by
yena.oh70 wrote:


I have loaded 16 fastq files - 15 of which were moved from another history, and 1 file which was recently loaded to galaxy through FTP.

I am only able to see the 1 file loaded through ftp when I attempt to run bowtie/tophat. On HISAT2 or fastQC, however, I see all 16 files. Any suggestions?


ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by yena.oh70
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Change the datatype to be fastqsanger. This is a recent upgrade: to auto-detect if fastq data is in fastqsanger format and assign that more specific type upon upload. Most tools expect fastqsanger and filter out other datatypes where fastq datasets are selected/input.

How-to FAQs here:

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
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