(1) Added functions to R DESeq scripts that output differential expression values for genes without a cutoff p-adj value applied. This is useful for generating JMP charts where all genes are included and only the significant ones are highlighted.
(2) Added function to Number_of_Reads_BLASTed.py that outputs reads which were not BLASTed successfully against the Macaque miRNA reference database so that they can be BLASTed to a Macaque ncRNA reference, in order to determine the percentages of reads which are rRNAs, snoRNAs, snRNAs, mt_rRNAs, or miRNA (multiple) or other ncRNAs.
(3) non_miRNA_BLAST_Parse.py parses the BLAST output for reads which did not successfully map to the Macaque miRNA reference and were thus mapped to the Macaque ncRNA reference to determine relative fractions of ncRNA types contaminating our miRNA data set.
Actually added non_miRNA_BLAST_Parse.py