Closed enricoferrero closed 9 years ago
The mean quality filtering is before adapter trimming while the end quality trimming if after adapter trimming. Thank you for your advice! I'll add this clarification to the skewer manual.
Sorry to hit up an old post, but it could help to have some clarification on the documentation:
Filtering & Post-trimming & Redistribution:
-q, --end-quality <int> Trim 3' end until specified or higher quality reached; (0)
-Q, --mean-quality <int> The lowest mean quality value allowed before trimming; (0)
For "The lowest mean quality value allowed before trimming", do you mean "...allowed before filtering"? It's not clear, at least to me, how --end-quality
is different from --mean-quality
, base on how the documentation is worded. It seems like --mean-quality
means: "if the mean quality of the read is < the cutoff, then filter the read", but the wording appears to be otherwise ("trimming"). Is there a way to filter a read (no trim) based on average read quality?
Can you please clarify here and in the documentation or help files at what stage the quality filtering/trimming is done? Is it before or after the adapter trimming?
From the help file:
From the output:
Thanks!