Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

BMC Genomics

Table 1 Contig retention through the screening pipeline for novel lncRNAs

Step	% Contigs Eliminated	# Contigs Eliminated	# Contigs Remaining
Orthology analysis (BLASTn)	62.7	54,405 (^a)	32,309 novel
Probable noncoding (CPAT p < 0.01)	70.1	22,781	9528
High confidence noncoding (CPAT q < 0.01)	98.1	9346	182
Pfam annotations	0	0	182
align to genome and compare to MAKER annotations	19.2	35	147

Columns as follows: “Step”, the name of the program or step in the screening pipeline; “% Contigs Eliminated”, the percentage of contigs from Column 4 of the previous row in the table that were eliminated in this step of the analysis pipeline; “# Contigs Eliminated”, the number of contigs corresponding to the percentage in Column 2; “# Contigs Remaining”, the number of contigs remaining after the row’s filtering Step was applied. The number of starting contigs before step 1 (“Orthology analysis”) was 86,714
(^a) This includes the 40 beaver contigs that we identified that are orthologs of known noncoding transcripts in other species (Fig. 9, purple rectangle). The percentage shown in column “% Contigs Eliminated” is for that specific step (row) relative to the number of contigs before that step.

ISSN: 1471-2164