PacBio: Subread Extraction with bash5tools.py

Question

[mehmetgoktay1989]

Hi Everyone,

I need to convert .h5 files to fasta/fastq files and need to filter based on subread length and quality score.

I have installed bash5tools.py and I was able to do what I wanted. But I am a bit confused.

After converting .h5 files to fastq and applying filtering. Do I still need to remove adapter sequences from fastq or fasta files?

[GenoMax]

BBMap has a removesmartbell.sh. You could try that on your subreads.

[mehmetgoktay1989]

Looks like SMRTbell adapter sequences were removed by the program. Thank you!

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to earlier posts, as such this thread remains logically structured and easy to follow.

Answer 1

[GenoMax]

SMRTbell adapter sequence is in this thread. If you don't see it then you are ok. There is also another suggestion of using find_artifacts.py from SMRTanalysis (if you have that available).