Question

Demultiplexing bcl files into fastq files

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6.7 years ago

Javad ▴ 150

Hello,

I have bcl formatted files generated by illumina nextseq 500 machine and I want to demultiplex them into fastq files. I can not install the software provided by illumina (bcl2fastq2) on my machine because apparently it is not compatible with ubuntu 16.04. Is there any other tool that can be used for demultiplexing bcl files?

Thanks in advance

RNA-Seq next-gen • 5.6k views

ADD COMMENT • link updated 6.7 years ago by chen ★ 2.5k • written 6.7 years ago by Javad ▴ 150

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Have you tried this solution for Ubuntu 14.04?

It sounds like boost 1.54 is the biggest complication.

ADD REPLY • link updated 4.9 years ago by Ram 43k • written 6.7 years ago by igor 13k

Ram · Answer 1 · 2017-08-25

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6.7 years ago

Dan D 7.4k

Picard has a BCL-to-FASTQ conversion tool that's not quite as robust as Illumina's proprietary tool. It might be worth a shot:

ADD COMMENT • link updated 4.9 years ago by Ram 43k • written 6.7 years ago by Dan D 7.4k

score 1 · Answer 2 · 2017-08-25

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6.7 years ago

chen ★ 2.5k

I am running bcl2fastq on ubuntu 14.04 and 16.04, both working well.

If you cannot run it, post the error messages here.

ADD COMMENT • link 6.7 years ago by chen ★ 2.5k

score 0 · Answer 3 · 2017-08-25

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6.7 years ago

GenoMax 141k

No that is your only option.

Someone recently installed it on ubuntu. Follow the discussion here: Issues installing bcl2fastq?

If this is a one time request you really should get the facility that produced the sequence to do the demultiplexing for you.

ADD COMMENT • link 6.7 years ago by GenoMax 141k

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Just out of curiosity: Isn't it normal that you get fastq from the facilities. We never had it that they provided the raw calls, unless especially requested.

ADD REPLY • link 6.7 years ago by ATpoint 82k