Export2Fastq Conversion
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13.6 years ago
Biomed 4.9k

Is there a tool other than the "Illumina software suite" that can convert illumina export files from illumina pipeline to fastq files that bwa can use as input?

fastq illumina next-gen sequencing • 5.3k views
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13.6 years ago

We convert the qseq output files from base calling into fastq, eliminating running GERALD and ELAND entirely. The output directory structure may be different depending on your version of the Illumina pipeline but with 1.6.0, the on-machine base caller will output qseq files in:

Data/Intensities/BaseCalls/

and the offline base caller (OLB) in:

Data/*_Firecrest*/Bustard*

The conversion from qseq to fastq is fairly straightforward. Here is a python script that produces fastq files from these qseq directories.

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hey this is great. Python is my primary choice too so it is a perfect match. I will look inti it and let you know what I could do with it.

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@Brad. Very nice and synthetic code. The ideas are beautifully expressed. I'll try to inspire myself of how you use tuple assignments (in the 'for' loops, eg: for a, b, c in x) to lighten your code.

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13.1 years ago

Here's a perl script I came across when somebody asked me this question.

Note: you may want to add a filter to remove reads with column 22 = N, those reads did not pass quality filtering.

Edit: This script is splitting on one or more whitespaces, which is wrong. Should be tabs.

As mentioned in the seqanswers thread referenced above, maq comes with a script fq_all2std.pl which had an export2sol option that works.

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13.6 years ago

I've never done it myself, but I know it can be done--the sequencing center we worked with last delivered us our data in both formats.

I did a quick search and this site came up. I'm guessing your answer is in there.

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hey thanks. I got that too but AFAIK Maq is Heng Li's old program and he is now developing BWA and SAMTOOLs. I couln't find the functionality in those packages nor in their miling list archives but it may be me that the functionality is there and I couldn't find it. If people are still usuing a Maq script or something else for this I would be glad to know. Thanks for the answer.

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7.9 years ago
ajguerras • 0

Hello everyone, I need 2 or 3 files in Illumina Export Format to test a software function, (size does not matter). I've been looking through all over the web and have not been able to find them. (I understand SRA don't use it). I tried to find CASAVA old versions in order to build my own files, but the software is not available anymore. Could anyone provide a couple of files, a link or suggest a repository ? Thank you very much, ....

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