BAM files, binary versions of Sequence Alignment/Map (SAM) format files, consist of alignments of DNA reads (generally short) to a reference sequence, usually a complete genome.
MAP-RSeq consists of alignment with tophat 2.0.6 (Kim et al., 2013, p.2) against the hg19 genome build and gene counts with the htseq software 0.5.3p9 (http://www.huber.embl.de/users/anders/HTSeq/doc/overview.html) using gene annotation files obtained from Illumina (http://cufflinks.cbcb.umd.edu/igenomes.html).html
To evaluate the performance of RNAstrand on alignments which have not been identified as structured RNA by RNAz, we constructed a second test set which only consists of alignments not classified as structured RNA by RNAz in both reading directions.
It is from dataset that we create the four optimized datasets as summarized in Table 2 and Figure 2. The first dataset, D s, consists of alignments with a single individual sampled per species at each locus (not necessarily the same individual across loci).
Up to this stage, the alignment consists of aligned representatives of NCIV clusters.
After these filters, the final data sets consist of 287 alignments covering 203 RNA families for EPO-35, 124 alignments covering 107 RNA families for EPO-12, and 182 alignments covering 149 families for Multiz.
Real gene alignment protocol consists of strict alignment (Bowtie, no mismatches, single alignment location) to the human genome (hg18, NCBI Build 36.1).
Pseudogene alignment protocol consists of strict alignment (Bowtie, no mismatches, report reads with only one alignment location only) to the composite genome.
These procedures typically consist of two stages; alignment rules and combination rules.
Concatenation methods concatenate the L alignments to create a single "super locus" consisting of an alignment of the m+1 species across L loci.
