Comments (7)
From [email protected] on June 07, 2011 00:59:12
Because cutadapt requires that you specify at least one adapter, you cannot use the -q option independently. For now, you can just specify an adapter that doesn't occur anywhere, like "XXXXXXX". Until I've decided whether to remove the requirement that at least one adapter needs to be given, I'll leave this issue open.
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From [email protected] on June 07, 2011 00:59:34
Labels: -Type-Defect Type-Enhancement
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From [email protected] on June 07, 2011 02:59:38
May i ask a question?
How do i set up the -q cutoff value? Is it based on Phred score(0~40) ?
felix
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From [email protected] on June 07, 2011 06:39:11
Yes. On FASTQ files, cutadapt assumes that quality values are encoded as ASCII(qual+33). See also this section from the README:
"The '-q' (or --trim-qualities) parameter can be used to trim low-quality ends
from reads before adapter removal. For this to work correctly, the quality
values must be encoded as ascii(phred quality + 33). If they are encoded as
ascii(phred quality + 64), you currently have to add 31 to the cutoff. For
example, if you actually mean "-q 10", you have to write "-q 41".
The trimming algorithm is the same as the one used by BWA. That is: Subtract
the given cutoff from all qualities; compute partial sums from all indices to
the end of the sequence; cut sequence at the index at which the sum is minimal."
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From [email protected] on June 07, 2011 11:01:41
You explained it in detail. Thanks a lot.
cutadapt is a very useful, powerful and simple to use.
felix
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From [email protected] on June 08, 2011 01:15:01
I'm happy to help, thanks for using cutadapt.
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From [email protected] on May 12, 2012 14:09:58
This feature has now been implemented and will be in cutadapt version 1.1.
Status: Fixed
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Related Issues (20)
- Error: BiocParallel errors HOT 5
- Remove the "Incomplete adapter sequence" warning
- Nanopore adapter detection HOT 1
- "OverflowError: FASTA/FASTQ record does not fit into buffer" when trimming ONT reads HOT 7
- Unexpected trimming behavior HOT 5
- cutadapt: error: cutadapt not able to trim the desired adapto HOT 3
- Error in FASTQ file at line 20136: Length of sequence and qualities differ HOT 2
- Adapter matches in the middle of a read masked with N HOT 2
- Feature request: shorten paired-end reads with separate values for --length HOT 1
- Help to get accurate counts of demultiplexed amplicons using cutadapt HOT 2
- Adapters in form of file and linked mode HOT 4
- Problems reading stdin on Windows 11 Python 3.12 HOT 5
- Heterogeneity Spacers and Primers HOT 2
- Using --revcomb on paired-end data HOT 1
- Issue importing fasta files to Cutadapt virtual environment HOT 1
- -m don't correctly work for pair-end analysis HOT 1
- Primer sequence trimming. Cutadapt does not cut all of them HOT 1
- Should I use -a or -g when demultiplexing ONT reads with dual barcodes? HOT 3
- Unable to trim primers from my interleaved fastq files HOT 4
- cutadapt not recognizing second input file HOT 1
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