Comments (6)
From [email protected] on February 08, 2011 03:19:28
Could you perhaps send me or attach to this issue an example of a FASTA and a QUAL file as produced by the Roche software?
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From [email protected] on February 08, 2011 04:07:29
For a short example (10 reads), see: http://biopython.open-bio.org/SRC/biopython/Tests/Roche/ or https://github.com/biopython/biopython/tree/master/Tests/Roche Original SFF file:
E3MFGYR02_random_10_reads.sff
The trimmed reads (what people normally work with):
E3MFGYR02_random_10_reads.fasta
E3MFGYR02_random_10_reads.qual
The untrimmed reads (with 454 adapter and poor quality bases):
E3MFGYR02_random_10_reads_no_trim.fasta
E3MFGYR02_random_10_reads_no_trim.qual
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From [email protected] on February 08, 2011 04:44:25
Thanks, I'll look into this. May take a few days.
Summary: Support FASTA + QUAL (not just for colour space)
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From [email protected] on February 14, 2011 06:58:34
I have added support for non-colorspace .FASTA+.QUAL files to cutadapt. It seems to work although the output is different from BioPython's trimmed sequences. This seems to be due to a different low-quality trimming algorithm. Remember to use the -b parameter to search for adapters that are potentially in the beginning of reads. If you don't, then all reads in which an adapter was found will be empty after trimming.
Can you get cutadapt from Subversion in order to test this? Otherwise I'll just release a new version.
Status: Fixed
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From [email protected] on February 14, 2011 08:01:18
The trimmed examples in the Biopython tests are just applying the trimming information in the SFF file itself (just like the Roche off instrument application does it).
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From [email protected] on February 15, 2011 10:46:31
Thanks, that also explains where the lowercase nucleotides in the untrimmed files come from.
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Related Issues (20)
- 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
- Update bioconda-recipe to support osx-arm64 HOT 2
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