This is a test version of Biostars. For the public version, visit https://www.biostars.org.
In the reformat tool of BBmap what is the meaning of Read1_linear and Read1_log

This is an example output from bbmap's reformat.sh tool using the following command:

 reformat.sh in1=input_R1.fq in2=input_R2.fq qhist=quality.txt

I've looked on the website and search biostars and seqanswers to try to understand what the column labels mean, with no luck.

#BaseNum    Read1_linear    Read1_log   Read2_linear    Read2_log
1   32.865  30.412  31.434  26.777
2   33.103  31.069  32.048  28.311
3   33.179  31.130  32.239  28.550
4   33.289  31.558  32.392  28.750
5   33.148  30.809  32.322  28.518

What is the meaning of Read1_linear and Read1_log? How are they calculated?

Thanks

bbmap quality reads
• 1,615 views • link
updated by h.mon h.mon • written by Joseph Hughes Joseph Hughes

Can you post the entire command? What were you trying to do?

• 0 views • link
written by GenoMax GenoMax

1 answer

These are the per-position base quality averages, calculated with different methods: the _linear is just the average of the Phred read qualities; the _log first translate the quality score to probability, then average of the probabilities, finally translate back to Phred quality score. I think the _log should better reflect the overall base quality than the linear, specially for data sets with large variations in qualities at the same position.

• 0 views • link
written by h.mon h.mon

Log in to answer this question.

More posts like this

No similar posts found.