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marcelm avatar marcelm commented on August 27, 2024

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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marcelm avatar marcelm commented on August 27, 2024

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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marcelm avatar marcelm commented on August 27, 2024

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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marcelm avatar marcelm commented on August 27, 2024

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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marcelm avatar marcelm commented on August 27, 2024

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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marcelm avatar marcelm commented on August 27, 2024

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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