Is specifyng -Q33 in fastx_clipper for Sanger/Illumina1.9 encoding fastq important?

[dena.dinesh]

Hi,

I have fastq files which as Sanger/Illumina1.9 encoding. When I clipped off the linkers I havent specified the -Q33 but still it trimmed the linkers. As I didnt mention the Q33 parameter, is my fastq files fit for further mapping?

Thanks in advance

[AntonioRFranco]

Q33 is a measure of sequencing quality. You can get more information from THIS LINK

You must get rid off of sequences that are badly sequenced because it will give you problems

[dena.dinesh]

Q33 is a measure of sequencing quality. You can get more information from THIS LINK

You must get rid off of sequences that are badly sequenced because it will give you problems

Thanks for your comment. In that case I think I should use -Q33 parameter whevener I Clipp or trimm the sequence using fastx right? Kindly guide me

[AntonioRFranco]

You must decide what value use to trim your sequences for quality
A filter of Q33 is pretty high. If you use that value, you will discard many useful sequences

Where is the border?

SOme users do a filtering of Q20, other Q25. Sometimes a compromise is required.

Use FastQC to get an idea of how many sequences you discard after filtering. FAstQC provides you with that information, and the graphics you get, are coloured with give you some simple explanation or valoration. Sometimes you simply make the sequences shorter, by discarding those sequences at the edge that are badly sequenced..

Look for tutorials about FastQC. You will find it very easy to use

[GenoMax]

All Illumina data (of recent vintage) uses Phred+33 offset (Sanger fastq format). If your data is in that format then you should specify -Q33 when using fastx. This option was not documented for fastx toolkit (it still may not be) and results in this oft asked question.