Question: How to know which illumina adapters trimm using BCL files
gravatar for patrick-douglas
3.2 years ago by
patrick-douglas0 wrote:

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?

ADD COMMENTlink modified 3.0 years ago by chen2.1k • written 3.2 years ago by patrick-douglas0

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 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).

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by GenoMax92k

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.

ADD REPLYlink written 3.2 years ago by h.mon31k
gravatar for chen
3.0 years ago by
chen2.1k wrote:

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.

ADD COMMENTlink written 3.0 years ago by chen2.1k
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