split_libraries_fast.py default behaviour

[francesca]

Hi there!

I used the split_libraries_fastq script and noticed in the log file many reads were discarded because "Read too short after quality truncation".

I couldn't find in the manual page which length is considered as cut-off and how modify it (while in the split_libraries.py script you can set your own cut-off value with the -l option). Is there any way to do the same when working with fastqs?

thanks

Francesca

[abir...@gmail.com]

Hi, Francesca,

For split_libraries_fastq.py, the minimum read length is represented as a fraction of the total read length, rather than an absolute number: see the documentation for the min_per_read_length_fraction switch at http://qiime.org/scripts/split_libraries_fastq.html .  The default is 0.75 of the read length.  Note that this approach anticipates that all reads will have the same length, so it just takes the length of the first read in the file as the read length.

Best,

Amanda