Overview of reads from raw data to cleaned sequences.

aAdapter dimer: 5′ ADT, 3′ ADT & 5′ ADT and 3′ADT joined together without insertion.
bJunk sequence: 80% of A, or C, or G, or T, or 3N; 10 repeats of dimer, 6 repeats of trimer, or 5 repeats of tetramer; 7 consecutive A, 8 consecutive C, 6 consecutive G or 7 consecutive T; contained only A and C or only G and T.
cSequences with length <16 nt or >26 nt were removed.
dSimple sequence: sequence with more than 80% of A, or C, or G, or T, or 3N in it.
eSequences passing mRNA, RFam, Repbase filter.
fmRNA: ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal2/bigZips/.
gRfam(V9.1): ftp://ftp.sanger.ac.uk/pub/databases/Rfam/9.1/.
hrepeat-repbase (V15.13): http://www.girinst.org/repbase/update/index.html.
Note: There is overlap in mapping of reads with mRNA, rRNA, tRNA, snRNA, snoRNA and repeats.