Hello,
I have paired end RNA-seq fastq files that has the quality score of the earlier version of Illumina, such as Illumina 1.5. I need to convert their quality scores to the one of Illumina 1.8.
I was wondering if there is any script available for this purpose before I start on it myself.
Thanks,
1 answer
Illumina 1.5 should be in Phred format. Do you mean you have older Illumina data in the +64 scale?
If you need to convert Illumina +64 to Phred +33 you can use a tool we have on GitHub.
Exercise caution, however, and make sure what offset you have. +33 is fine. +64 can be converted. The even-older Illumina format uses log-odds, and is not the same conversion. The FastQ wiki article may help you sort all this out. And I believe FastQC reports the quality scale when you run it anyway.
Log in to answer this question.
-
How to extract the mean quality score of RNAseq for a sample?
written by Youyy •
-
Converting Illumina fastq quality scores to phred
written by L. A. Liggett
-
Trimming read length & quality in a FASTQ file
written by ChIP
-
Convert Phred score 41 to 40
written by Biomonika (Noolean)
-
Fastq-Dump Quality Scores Off Scale
written by Clare
-
Fastq Illumina 1.8+ And Sanger
written by arkarachai.af •
-
What Is The Default Quality Encoding Expected By Bwa?
written by Panos
-
Does Illumina Paired End Reads From Rna Seq Need To Be Groomed?
written by Preaslio •
-
Fastq Format Problem When Using Bwa Aln -Q Option (Read Trim)
written by Bioscientist
-
Trim The Low-Quality End Of 100Bp Read
written by Bioscientist
I found this solution:
This can be done with standard tools, e.g. EMBOSS (the program 'seqret'), BioPython, or BioPerl. Check the "similar posts" to the right, or search "illumina to sanger" and you will find many solutions. Personally, I would just use a standard tool since they all agree.