Q33 in fastx_clipper

Question

[EVR]

Hi,

I am working RNAseq data which is strand specific and read length ranges between 25bp-32bp. After demultiplexing, I removed the the linker sequence using fastx clipper without specifying -Q33 parameter like

fastx_clipper -a <linker_sequence> <input_fastq> <linker_removed_fastq>

I haven't specified -Q33 but I didn't got any error. Is the outputted sequence is free of linker? Is it really mandatory to specify the -Q 33 parameter?

Kindly guide me

[EVR]

My fastq files has Phred 33, so in that case should I use -Q33 in fastx_clipper and fastx_trimmer

[pld]

Yes, you should.

Answer 1

[pld]

No, the Q33 parameter is only for when you're dealing with sanger quality scores.

[EVR]

Thanks for your guidance. How to find that whether my fastq files has sanger quality or not?