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Adapter sequences not removed from short SE data #577

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MafGal opened this issue Sep 26, 2024 · 0 comments
Open

Adapter sequences not removed from short SE data #577

MafGal opened this issue Sep 26, 2024 · 0 comments

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@MafGal
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MafGal commented Sep 26, 2024

Dear fastp team,
First of all thank you for the tool, very nice!

I am running fastp on SE data from a smallRNAseq dataset of 50nt reads, provided the default adapter sequence "TGGAATTCTCGGGTGCCAAGGC" and minimum length 15.

Although fastp finds many of the adapter sequences, it is not removing them.
Screen Shot 2024-09-26 at 11 40 31

Why is this happening / how to get files with all adapter sequences/subsequences trimmed?
Screen Shot 2024-09-26 at 00 22 22

This is my code:
`Adapter2remov="TGGAATTCTCGGGTGCCAAGGC"

threads=4

fastp -w $threads -i "$file" -o "${file/.fastq.gz/_fastpadapt30_2.fastq.gz}" -h "${file/.fastq.gz/_fastpadapt30_2.html}" -j "${file/.fastq.gz/_fastpadapt30_2.json}" --low_complexity_filter --complexity_threshold 30 --average_qual 30 --qualified_quality_phred 30 -5 -3 -r --trim_poly_x --poly_x_min_len 6 --trim_poly_g --poly_g_min_len 6 -z 4 --adapter_sequence "$Adapter2remov"`

Thanks in advance for the help,
Mafalda.

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