Question

Q33 in fastx_clipper

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9.5 years ago

EVR ▴ 610

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

Fastx RNA-Seq • 2.5k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by EVR ▴ 610

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

ADD REPLY • link 9.5 years ago by EVR ▴ 610

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Yes, you should.

ADD REPLY • link 9.5 years ago by pld 5.1k

Ram · Answer 1 · 2015-06-11

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9.5 years ago

pld 5.1k

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

ADD COMMENT • link updated 23 months ago by Ram 44k • written 9.5 years ago by pld 5.1k

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

ADD REPLY • link updated 23 months ago by Ram 44k • written 9.5 years ago by EVR ▴ 610