fastx quality score

[madsaan]

Hi ,

I am new to NGS analysis and trying my hand at fastx toolkit.I am trying to assess the quality of my sequence and part of the result is below.I would like to know the following

1.should we consider the mean column for assessing the quality of each cycle?
2.what is the minimum value below which the quality is considered bad?is it 20?


column count min max sum mean
1 10357317 2 40 404977359 39.1
2 10357317 2 40 404775168 39.08
3 10357317 2 40 404764272 39.08

your help will be greatly appreciated!!

Thanks,
Joji

[simonandrews]

In general the mean quality is not a great measure since the distribution of quality values for a cycle is far from normal. The median is somewhat better, but I generally prefer looking at the 25th and 75th percentiles to try to get a better impression of the range of qualities in a cycle. You often find that the 25th percentile can drop to nearly zero, whilst the 75th percentile is still very high.

The cutoff for bad quality is often taken at 20 since this represents a 1% error rate, but these days I'd expect much better than that. I'd normally expect qualities of >28 for a good run. If I saw Q20 reads I'd be looking to see what the quality was so poor. (This may vary on different sequencing platforms though).

[madsaan]

thanks for the reply.My q1 values start at 40 and end at 32.My q3 values start at 40 and end at 38.That means 25% of the scores are below the corresponding value for each cycle.Then how will I know if it is less than 28.The reason why am asking this is because I would like to know if it is ok for me to proceed with velvet assembly without modifying the fastq file.

Thanks,
Joji