high complexity reads removed

[theo-allnutt-bioinformatics]

Hi,

I have an issue with high complexity reads being removed. I am using fasta input because I am only interested in the complexity , not quality.

The files are here:
https://drive.google.com/open?id=1IHfERmzQauE3XNVVzaPU4yLg7dWe5Bmo

command:
InfoTrim.py 69.fasta -o 69_infotrim.fasta --fasta --min_length 100 -p 12

The file 69_trimmed.fasta contains the reads from the original (69.fasta) that were removed in 69_infotrim.fasta.

A quick look at these reads shows that they are not low complexity. I really only want to remove or trim sequence that is'mostly' homopolymer or simple repeat.

Thanks,

Theo

[JacobPorter]

InfoTrim typically trims the ends of the reads, but it can trim the beginning of the read as well if another algorithm is chosen. So, it isn't really a filter; it is a trimmer.

The files 69_infotrim.fasta and 69_trimmed.fasta each have 50000 reads of I think the same size. This is not output that InfoTrim would produce.

You can try setting -r to a value higher than 0.4 so that InfoTrim will increase the entropy term weight in its score, but it looks like you are really looking for a low entropy filter rather than a trimmer. Perhaps a different program would work better.