Comments (1)
From [email protected] on January 17, 2011 00:06:43
Very little information is lost and actually cutadapt has no other choice. The AB SOLiD white papers and lots of papers about color space alignment document why the alignment has to be done in color space (that is, with 0, 1, 2, 3). If the adapter is sequenced without errors, its color space sequence will always be 330201... (plus maybe some errors). You are correct that the inverse is not true: If 330201... is seen, then this is not necessarily the adapter -- but it probably is. You have the same problem with sequencing errors: If 331201... is seen, this does not have to be the adapter, but it probably is.
This is not a problem or a defect, it is a property of color space alignment, I'll therefore mark this issue is "invalid" for now. If you think this is incorrect, please reply.
Status: Invalid
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Related Issues (20)
- Add --trimmed-poly-a-only for poly-a as --trimmed-only for adapter
- cutadapt pair-adapters almost all sequences end up in the unknown fastq files HOT 11
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- Small ONT optimization: length filtering before applying trimming HOT 1
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- Catching ONT adapters: allow setting insertion and deletion scores HOT 4
- paired fasta input with multiple cores HOT 7
- Feature request: ONT Chimeric read splitting HOT 1
- KmerFinder: x of length y is longer than the maximum of 64 HOT 1
- Question about the paired-end read trimming. HOT 1
- Installation instructions need conda channel HOT 2
- poly-A trimming for paired-end data - consider orientation HOT 2
- sc/snATAC-seq barcode correction HOT 5
- ERROR: Error in sequence file at unknown line: Reads are improperly paired HOT 2
- Make Cutadapt portable on macOS HOT 11
- feature request: ubam support? HOT 4
- NextSeq Quality Trimming Issue HOT 3
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- Use `--action=lowercase` for short reads but keep trimmed passed reads. HOT 2
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