How to know which illumina adapters trimm using BCL files
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4.2 years ago

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?

RNA-Seq sequencing next-gen ChIP-Seq • 2.2k views
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Unless you have the full data folder available converting then BCL files to fastq will not be trivial. Can you ask your sequence provider to do the conversion for you? It would be significantly simpler to manage the fastq files from that point onwards.

You could use a file with all commercial adapters (e.g. adapters.fa file as supplied with BBMap suite). It may cause a bit of overtrimming but does not require you to know the exact adapter kit in advance. If you have paired end reads that overlap then it is possible to identify adapters using bbmerge.sh program from BBMap suite. FastQC contains the relevant adapter references and by running that your fastq files you may be able to identify specific illumina kit used (as long as they are present in enough numbers).

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If you have the samplesheet, and the adapters are standard Illumina adapters, you can trim them on the fly while converting bcl to fastq with bcl2fastq2.

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4.0 years ago
chen ★ 2.3k

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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5 weeks ago
Jiacheng ▴ 10

It is recommended to use bcl2fastq first without providing adapter sequences. Then, you can use many trimmers to trim adapters.

I'd recommend atria to determine and trim the adapter sequences. It is a cutting-edge trimmer with exceptional precision and speed.

atria -r reads.fastq ... --detect-adapter
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Please do not revive old posts to promote tool authored by you. Start a new post under tool category. It seems you are first author on the manuscript of this tool.

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yes, due to excessive repeating content some of the posts have been marked as spam. I have restored most posts.

The author was primarily trying to be helpful with the post not understanding the proper protocol.

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