Question: Q33 in fastx_clipper
0
gravatar for EVR
4.4 years ago by
EVR560
Earth
EVR560 wrote:

Hi,

I am working RNAseq data which is strand sepcific 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 havent specified -Q33 but I didnt got any error. Is the ouputted sequence is free of linker? Is it really mandatory to specify the -Q 33 parameter?

Kindly guide me

 

 

rna-seq q33 fastx • 1.2k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 4.4 years ago by EVR560

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

ADD REPLYlink written 4.4 years ago by EVR560
1

Yes, you should.

ADD REPLYlink written 4.4 years ago by pld4.8k
1
gravatar for pld
4.4 years ago by
pld4.8k
United States
pld4.8k wrote:

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

ADD COMMENTlink written 4.4 years ago by pld4.8k

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

ADD REPLYlink written 4.4 years ago by EVR560
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