Comments (5)
sfchen
commented on August 29, 2024
Currently fastp doesn't trim polyG with G number less than 10. If you prefer a parameter to adjust this setting, I will implement it in the coming version.
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mht85
commented on August 29, 2024
It would be nice to have the option to adjust that setting. Would also be great to have the count included in the report? Just a suggestion. Thanks for the software by the way. May I know when the next version will be released?
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sfchen
commented on August 29, 2024
Next revision will come in two weeks.
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sfchen
commented on August 29, 2024
With the latest version in the master branch, you can use --poly_g_min_len to change the minimum length requirement for polyG detection. By default it's 10.
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sfchen
commented on August 29, 2024
Any update? Have you tried the new fastp, which can be compiled from the latest code, or downloaded from http://opengene.org/fastp/fastp ?
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Related Issues (20)
- Not able to install on Mac book M1 HOT 4
- Keep occurred error message from the beginning < igzip: invalid gzip header found >
- Nanopore data filtering using fastp HOT 1
- No adapter detected for read and Q20 bases: 4747174600(99.9999%)
- fastp not removing all Illumina universal adapter sequences as indicated by FastQC HOT 4
- few options throw 'undefined error' -reg
- Error is raised for problematic rows HOT 3
- not support arm? HOT 1
- Not reproducible HOT 7
- Running fastp in quiet mode. HOT 2
- Feature Request: fastp operation on input and output directories
- ERROR: '+' expected HOT 5
- Feature request: remove reads with poly_X tails and polyX in general
- typo in "forogt" -> "forgot" HOT 1
- How can I generate images of the same size as the insert fragment individually
- Feature request: output file listing the IDs of duplicate reads and associated "representative reads" HOT 1
- How can I reproduce the results of trimmomatic in fastp?
- Use with fifo? HOT 3
- trimming adapters at the beginning of the read and IUPAC nucleotide codes
- Ability to use FASTA files as input
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