Comments (3)
To follow up on this: I tried trimming using the example data again but without specifying the adapter sequences and the reads were not trimmed. So to clarify the issue, it is with spurious match of the adapter to the read. I think you need to add the equivalent of the -O parameter in Atropos and Cutadapt. Also note that, with the alternate option I describe above (using random match probability), Atropos uses a heuristic (that was copied from SeqPurge) to require both adapter sequences to match their respective reads when the match length is <= than some threshold (9 bp by default), regardless of the probability. This seems to be necessary to achieve good performance with short adapter matches.
from fastp.
Thank you John.
In current implementation, fastp
will trim the reads if it matches the adapter with 4 or more bases in 3' end. This may introduce a bit overtrimming (may overtrim <0.1% of the data for 150bp reads), but will definitely give cleaner data.
It's a good idea to expose a parameter to change this setting. I will implement this in next release.
from fastp.
When can we expect this new feature to be released? The -O option in Cutadapt is really useful.
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Related Issues (20)
- Can fastq remove read sequences with duplicate IDs?
- Feature request: add option to set lower limit of unqualified quality
- Missing most reads after given r2 adapter HOT 1
- Interpretation help file?
- Store duplicate reads
- Split interleaved output
- interleaved output is not reproducible with multiple threads HOT 2
- 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
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