Trimming reads with prinseq
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3.9 years ago
deepti1rao ▴ 40

What quality trimming options can be used with prinseq? I intend to use a min qual of 20 and would like to trim from the right and retian those reads that have a min length of 30. What window size is good? I want to de novo assemble a genome with these reads.

Forward reads fileReverse reads file

prinseq reads preprocessing qual trim • 2.4k views
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My reads are 150 bases long. Chan, do you suggest 6 as the sliding window? How does one decide?

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I think 4~6 window size is good to try with.

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Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

This should have gone under @Chen's answer below.

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3.9 years ago
GenoMax 108k

You can check the manual/in-line help for prinseq program to get this type of information.

I would recommend that you use bbduk.sh from BBMap suite. You can easily understand options you need. e.g. in your case trimq=20 minlen=30.

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3.9 years ago
chen ★ 2.3k

fastp is a good tool for your task. Run fastp with:

fastp -i in.fq -o out.fq -3 -W 6 -M 20 -l 30

-i in.fq specifies the input fastq file
-o out.fq specifies the output fastq file after filtering
-3 enables the sliding window cutting in 3'
-W 6 specifies 6 as the sliding window size for quality cutting
-M 20 specifies Q20 as the mean quality requirement within the sliding window
-l 30 indicates that reads shorter than 30bp will be discarded

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