Reads quality scoring system used ??

[rahularjun86]

Dear all,
As most of the NGS data analysis packages(Bowtie2, Sickle,...) depends on the reads quality scores, Is there any tool/package to predict the quality scores used for the raw reads?? I was trying this with unix grep and then checking the ASCII tables for ranges used in my raw reads.
Many thanks,
Rahul

[chadn737]

What sequencing platform?

[rahularjun86]

I have two lanes of paired end Illumina reads. One lane sequenced after 1 and half year. Using grep, I am getting symbols having ASCII value staring from 35 in lane1(Phred quality score) and in another lane the values are starting from 64(Illumina 1.3+).

[chadn737]

Starting with CASAVA 1.5+ used phred+64 but with CASAVA 1.8 they switched to phred+33.

Check out this thread:

http://seqanswers.com/forums/showthread.php?t=8895

[Heisman]

If you run it through FastQC it will output the quality score system it detected.

Also maybe look here: https://www.uppnex.uu.se/content/che...y-score-format

[rahularjun86]

Dear Heisman and chadn737,
Many thanks for your great help, I will try these methods soon.
Best regards,
Rahul