Demultiplexing bcl files into fastq files
3
0
Entering edit mode
7.3 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 • 5.9k views
ADD COMMENT
0
Entering edit mode

Have you tried this solution for Ubuntu 14.04?

It sounds like boost 1.54 is the biggest complication.

ADD REPLY
1
Entering edit mode
7.3 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
1
Entering edit mode
7.3 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
0
Entering edit mode
7.3 years ago
GenoMax 148k

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
1
Entering edit mode

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

Login before adding your answer.

Traffic: 1934 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6