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option to remove reads that fail the Casava filter #107

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marcelm opened this Issue Mar 14, 2015 · 4 comments

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marcelm commented Mar 14, 2015

From jkgren...@gmail.com on February 10, 2015 17:22:41

Hi,
I use cutadapt to trim Illumina reads for adaptor sequences and low-quality bases. I would love to also have the option to filter out reads that fail the Casava 1.8 filter ("Y" in sequence id line) since the fastq files I receive contain failed reads.
Thanks for considering this (easy) filter,
Jen

Original issue: http://code.google.com/p/cutadapt/issues/detail?id=97

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marcelm commented Mar 14, 2015

From marcel.m...@tu-dortmund.de on February 11, 2015 05:17:20

Give me a few days to think about this. Sure, it’s easy to implement, but it does not have to do anything with adapter trimming per se. But then quality trimming, which cutadapt also does, is also not really adapter trimming ...

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marcelm commented Mar 14, 2015

From jkgren...@gmail.com on February 11, 2015 06:20:17

Thanks for considering. I like to use cutadapt as a high quality, tunable one-stop-shop for preprocessing, including adaptor trimming, quality trimming, length filtering (post-trim), and (ideally) Casava-filtering. Saves me time not to have to do each step separately, since I/O is the slow part!

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marcelm commented Mar 14, 2015

From marcel.m...@tu-dortmund.de on February 11, 2015 06:54:32

I understand because that’s how I like to use cutadapt myself ;-). However, disk I/O shouldn’t be an issue even if you use multiple programs since you can use a pipe to connect them together, similar to this:

my-casava-filter-program input.fastq | cutadapt -a ADAPTER - > output.fastq

(Assuming here that my-casava-filter-program writes the reads to standard output.)

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marcelm commented Mar 14, 2015

From jkgren...@gmail.com on February 11, 2015 07:39:10

True! But there arent any (good) Casava-filtering programs out there (that
I could find). I wrote a quick awk script but Im not really a programmer.
Imight also have to pipe through gzip (twice) to handle the fastq file
de/compression.
Anyway, thanks for considering, its certainly true there are other options!

@marcelm marcelm closed this in 34a8b56 Apr 30, 2018

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