PacBio: Subread Extraction with bash5tools.py
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?
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mehmetgoktay1989 •
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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).
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BBMap has a
removesmartbell.sh. You could try that on your subreads.Looks like SMRTbell adapter sequences were removed by the program. Thank you!
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