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                        Spidermite small RNAs analysis
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Eric Bonnet
erbon@psb.vib-ugent.be


Files:
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tRNA_coord: 
  Coordinates for tRNAs (predicted with tRNASCAN-SE).
  139 sequences.

rRNA_coord:
  Coordinates for rRNAs (predicted with RNAmmer, using specific cutoff).
  56 sequences.

infernal_ncRNA_coord: 
  Coordinates of tRNAs, rRNAs, snoRNAs, snRNAs, U-RNAs, predicted with infernal,
  and parsed with a cutoff score of 28 bits.
  357 sequences

uniq_coord: 
  Coordinates of unique small RNA sequences after filtering.
  676,266 sequences.

Filtering steps:
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- select reads with length >=18 nt
- filter out sequences with more than 3 Ns
- filter out sequences having long single nucleotides repeats (sequence of 10
  A,T,G,C)
- filter out sequences having less than 3 counts
- map seq to spidermite genome ("old" assembly), requiring perfect alignments
  (blastN with appropriate parameters).
- filter out sequences overlapping with tRNAs, rRNAs, snoRNAs, snRNAs, URNAs
  (predicted using tRNAscanSE, RNAmmer and infernal, with appropriate cutoff
scores).
- group unique sequences from each GES pool (and keep a table of
  correspondences)