Overview of reads from raw data to cleaned sequences.

a<p>Adapter dimer: 5′ ADT, 3′ ADT & 5′ ADT and 3′ADT joined together without insertion.</p>b<p>Junk 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.</p>c<p>Sequences with length <16 nt or >26 nt were removed.</p>d<p>Simple sequence: sequence with more than 80% of A, or C, or G, or T, or 3N in it.</p>e<p>Sequences passing mRNA, RFam, Repbase filter.</p>f<p>mRNA: <a href="ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal2/bigZips/" target="_blank">ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal2/bigZips/</a>.</p>g<p>Rfam(V9.1): <a href="ftp://ftp.sanger.ac.uk/pub/databases/Rfam/9.1/" target="_blank">ftp://ftp.sanger.ac.uk/pub/databases/Rfam/9.1/</a>.</p>h<p>repeat-repbase (V15.13): <a href="http://www.girinst.org/repbase/update/index.html" target="_blank">http://www.girinst.org/repbase/update/index.html</a>.</p><p>Note: There is overlap in mapping of reads with mRNA, rRNA, tRNA, snRNA, snoRNA and repeats.