How to know which illumina adapters trimm using BCL files
I have BCL2 files of transcriptome sequenced in the Hi Seq illumina platform, but I don’t know the Illumina library prep Kit.
The is any way to know which adapters to trimm directly from BCL or FASTQ files?
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You can use fastp to trim adapters for Illumina sequencing data, without the need of knowing the adapter sequences.
Just download fastp and run:
fastp -i in.fq -o out.fq
And then everything is done, the adapters are trimmed in out.fq
For paired end data, the command is like:
fastp -i in1.fq -o out1.fq -I in2.fq -O out2.fq
Gzip is supported for both input and output.
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