HI
My trimmomatic analysis shows this error, Please what can I do?
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/47313312/_job_tmp -Xmx28g -Xms256m
TrimmomaticSE: Started with arguments:
-threads 8 fastq_in.fastqsanger fastq_out.fastqsanger SLIDINGWINDOW:4:20
Error: Unable to detect quality
Hi @ERNEST_KISSI
it looks like an issue with input files and/or datatypes. Cab you preview the input FASTQ files? What datatype (value after format:) is assigned to the file(s)?
If you share the history, I or someone else can have a look. History sharing: history menu (icon at the top right corner of the history panel) > Share or publish > Make history accessible > copy and paste URL here. You can unshare it later.
Kind regards,
Igor
Here is the link
The file that I am trying to trim has been named TRIM
Hi @ERNEST_KISSI
Trimmomatic (is a) flexible read trimming tool for Illumina NGS data, while you have long reads with very wide range of Phred quality scores - check it with FastQC. Do you use PacBio reads? For additional information on Phred quality score check Encoding section in FASTQ format - Wikipedia
Try fastp instead of Trimmomatic: it does trimming and filtering for long reads and less sensitive to wide range of Phred quality scores. It also does QC. You may also check other tools designed for long reads.
You can unshare the history, unless you have other questions on the issue.
Kind regards,
Igor
Thank you but this is my school assignment and I am supposed to use trimmomatic on a server but unfortunately I have no command line experience and I wanted to use Galaxy instead. Thank you very much for the help. Much appreciated, Igor
hi @ERNEST_KISSI
fastp is available on public Galaxy servers, hence no need for command line use.
I don’t see any issue with your FASTQ file, but it is not compatible with Trimmomatic in Galaxy because of extended range of Phred quality score. I reduced the range of Phred quality score on a PacBio read, to match ‘illumina’ range, and Trimmomatic has no issue with that data.
Kind regards,
Igor
Hello Igor,
Can you help me once again?
I am trying to find the % of aligned reads and average coverage in a sam file that I got after doing mapping
Hi @ERNEST_KISSI
Some tools produce mapping stats, in additional Summary file.
Maybe have a look at tools like QualiMap BamQC.
Also, consider checking relevant Galaxy tutorials at https://training.galaxyproject.org/
Kind regards,
Igor
Thank you for your response
HI
Is there a tool in Galaxy to assess operons and visualize opens?
Again, how can I detect whether a gene has underwent horizontal transfer using galaxy.
Lastly, finding genes associated with secondary metabolites.
Hi @ERNEST_KISSI
it seems these questions are about research process. Find tools used for these tasks in recent publications and check if the tools are available on public Galaxy servers.
If you have annotation of operons, maybe try visualization using JBrowse. Galaxy Training Network has several tutorials with JBrowse.
Hope this helps.
Kind regards,
Igor