Hi all,
I am analyzing raw data of Illumina reads for bacterial (Wole Genome Sequencing) using tools on the galaxy website. I used trimmomatic, and trim-Galore to remove adapters and low-quality readers.
Fastqc analysis of trimmed reads gave me this report!
Summary
Basic statistics
Per base sequence quality
Per base sequence content
Sequence Length Distribution
Sequence Duplication Levels
Previously, I faced a problem with Nexttera Transposase sequences, but it was solved by using Trim-Galore as recommended,
1- So, Please give me your evaluation! Is it ok to use this reads for assembly!, or I should improve the quality!!, and how can I improve it!
2- Also, is it enough to assemble the paired reads, or I should also process unpaired ones as well!
Thank you for your time
The link you posted is broken. I edited your title, please use short, meaningful titles in the future.
Depends on how much coverage you have, but generally, using just the paired ends is enough.
thanks, h.mon, I modified the post...
The images still appear to be broken. Please post correct links.
I re-uploaded the photos
Don't set an auto-delete time, if you were doing that.
BTW: Data looks reasonable. If the adapters are gone then you can try doing the assembly.
I Modified it again, thanks
I don't know if you can provide custom sequences to trimmomatic via galaxy interface. But that would be the way to go to tackle.
I suggest that you use How to add images to a Biostars post to post images from FastQC report.
FastQC authors have some blog posts that are a good read to understand some of the observations you have noted.
thank you genomax for the link, it is very useful
If you are using galaxy you could try trimgalore. This tool already has a parameter specifically for Nextra Transposase
Thank you gb, I used trim-galore and it successfully removed these adapters