I am trying to classify a fastq read file with MetaPhIan2 When I run MetaPhIan2, the result is 100% unclassified. Then I transform the fastq to fasta, run MetaPhIan instead, and I get a right classification (100% Cyanobacteria). I assume that there is some problem with the fastq file but do not know which one, since the fastq file is correct and works for assembly and bowtie mapping that I did externally. Any help will be appreciated. Thanks!
Double check that your fastq data is in
fastqsanger format. This is the required fastq input format/content for Galaxy-wrapped tools. During Upload, this datatype is automatically assigned when "autodetect" is used and the data is a match for the quality score scaling.
If you are loading the data compressed and preserving that by directly assigning the compressed variation of the same datatype (
fastqsanger.gz), it may not really be in
fastqsanger format. You'll need to confirm that (run FastQC).
- Galaxy FAQs: https://galaxyproject.org/support >> https://galaxyproject.org/support/#getting-inputs-right
- Galaxy Tutorials: https://galaxyproject.org/learn/ >> https://galaxyproject.org/tutorials/ngs/
Thanks! Jen, Galaxy team