FastQ files - Is the content of the + line requiered or I can get rid of it?
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8.4 years ago
BioApps ▴ 790

I am building a visual FastQ editor (An efficient FastQ viewer and editor (GUI)). I hope it will be the mother of all fastq graphic editors :). I started to implement some functions already and to write output to disk. So, I have a question: is the content of the + line necessary? If I don't save that content the resulted file will be 25% smaller, which is a HUGE difference!

@SR000066.212673 EQ length=115
ACGT
+SR000066.212673 EQ length=115           <-------- remove this content (keep +)
B:B:

I have seen an article saying that it can and should be removed. Since there is no official documentation for FastQ format, I think that MAYBE some tools out there may still use that field for god-knows what.

fastq • 2.0k views
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Yes, a good practice is to remove it, to reduce the file size and the memory required to open it.

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My FastQ Editor always requires the same amount of RAM (below 25MB) no matter how big the files it is.

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8.4 years ago
Assa Yeroslaviz ★ 1.7k

As far as I know, you can remove the content if you keep the structure. There are already some fastq files, were you only have the '+' symbol with no content.

BTW - is your tool still only for window machines?

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Hi Frymor - The 'documentation' says indeed that the data in + field is indeed optional.

>Is your tool still only for window machines?

Yes. For the moment it only compiles on Windows. But don't worry; there will be a Mac and then Linux version also.

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+1 I have never used the third line for anything, and Illumina sequencers leave it empty except for the '+'.

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8.4 years ago

I can only think of one operation that would benefit from this commented strand entry, and that is generating FASTA + QUAL files from your FASTQ file (simply split every two lines and replace @ and + with >). Since none of us do that operation routinely I don't think you'll miss out on much.

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I think I better add a checkbox to let the user decide, but let the checkbox unchecked by default.