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ILLUMINA & AB SOLiD miRNA IsomiR VIEWS
build:   0.8
CONTACT: tfehnige@DOM.wustl.edu
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This directory contains miRNA isomiR views for mouse NK cell resting and
activated samples. The directory structure is setup for localized viewing in a
web browser, offline. To display, view any of the following HTML indexes in a
web browser:

     ill_known_plus.html
     ill_novel_minus.html
     ill_novel_plus.html
     solid_known_plus.html

Each index is composed of a table of miRNA "clusters" formed by alignment to
known (miRBase) miRNAs or novel candidate target references. Clicking on any of
the "HTML" links will open the corresponding cluster/miRNA isomiR views for
display. Clicking on the "plaintext" link will access the same view without any
HTML mark-up.

The following ancillary files of interest are included, for novel Illumina
isomiRs, in this build.

     NOVEL.probcalc.filtered.gt10.e06.wSEQ.fixed
     STRAND-BREAKDOWN-ILLUMINA-KNOWN.tsv
     STRAND-BREAKDOWN-ILLUMINA-KNOWN.xlsx
     STRAND-BREAKDOWN-ILLUMINA-NOVEL.tsv
     STRAND-BREAKDOWN-ILLUMINA-NOVEL.xlsx

NOVEL.probcalc.filtered.gt10.e06.wSEQ.fixed:
Illumina "novel" alignments as produced by the SHRiMP aligner; these alignments
are based on "squashed" or compressed query sequences. Fields follow the general
SHRiMP probcalc output format: readname; contigname; strand; contigstart;
contigend; readstart; readend; readlength; score; editstring; normodds; pgenome;
pchance.

STRAND-BREAKDOWN-ILLUMINA-*:
Strand breakdown files based on alignments with the SHRiMP viewer and the
corresponding orientation of the alignment in respect to the target or known
miRNA reference sequence (always 5' --> 3' in orientation). Both Microsoft Excel
and tab-separated versions of the file are included. Fields are: strand call;
majority vote; # alignments; # desquashed reads; (+) desquashed reads; (-)
desquashed reads; cluster ID.


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