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?
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.