Sequence loss


I was just wondering what % of sequencing is acceptable to lose before the screen command and after filter.

Before screen I have 103000 unique, 125000 total sequences

and after filter…then unique… I have 86 000 total sequences and 23 000. Is this too big of a loss?


So you’re losing about 30% of the reads. Whether that’s a lot is up to you. How long are the sequences? The tradeoff is between read numbers and read length.

Also, if you are using the shhh.flows approach in the Schloss SOP, all of your sequences should be close in length.

Hope this helps,