UNR-CFB / lahontan

Lahontan: a flexible, multiscale RNA-seq pipeline
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add iterative/progressive fastqc vecscreen trimmomatic workflow #16

Open rltillett opened 8 years ago

rltillett commented 8 years ago

As follows, more or less:

  1. trimmomatic module IDs over-represented sequences
  2. add polyNs (or polyN, length m minus k, where m=observed and k is chosen) to custom trimmomatic library
  3. locally run blastn vs. univec using vecscreen-like mode
  4. add hits to custom trim library and custom fastqc adapter/contam library
  5. trim w/ just-made custom libraries
  6. repeat if new vector found & added (always from original input files? might be best)

    Vecscreen mode

According to secret info I nabbed from ncbi

The VecScreen parameters are pre-set using blastn options: -task blastn -reward 1 -penalty -5 -gapopen 3 -gapextend 3 -dust yes -soft_masking true -evalue 700 -searchsp 1750000000000