I am trying to analyze microRNA sequencing data for 8 datasets ( each dataset is a cell line). I am able to run FASTQC and Multi-QC. Single end data.Per sequence quality, 8/8 passed. Sequence duplication level 8/8 failed.Persequence GC content 8 failed. So When I tried to use TRIMMOMATIC, it is showing error in the collection. Please advice. here is the error message Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/018/565/18565857/_job_tmp -Xmx7g -Xms256m TrimmomaticSE: Started with arguments: -threads 1 -phred33 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20 Exception in thread "m
I am not sure how you extracted/manipulated the data before uploading it, but it has a formatting problem. The line count is not correct for fastq data (must be a multiple of 4) and at least one sequence is has a problematic sequence identifier (the "@" is missing). Not all tools result in an error using this input, but many will. It is best to get a clean copy of the source fastq data.
To extract these reads directly into Galaxy, use the tool NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA. All you need to enter on the tool form is the accession number.
Support FAQs: https://galaxyproject.org/support/#getting-inputs-right
Thanks! Jen, Galaxy team