NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites

BMC Genomics

Table 1 Summary of sequencing and alignment results

Samples^a	Adaptor Sequence^b	Number of Raw Reads (×10⁶)	Uniquely Mapped Reads^c (×10⁶)	% rRNA Reads^d	Redundancy^e	Average # of Genes with TSS Peaks (×10³)^f	Average # of Peaks per Gene^g
Exp. 1
S1BALA	GGG	183	123	0.29	3.73	10	1.23
Exp. 2
S2BPLP	ATCGTG GCTATA GGG	61	17	2.90	2.08	15	1.3
S3BPLP	GATCGA GCTATA GGG	26	5	2.15	1.93	12	1.13
S4BPLP	TCGAGC GCTATA GGG	37	6	2.44	1.98	13	1.18
Exp. 3
S5BPLA	CAGATC GGG	18	14	16.05	2.84	7	1.13
S6BPLA	CCGTCC GGG	15	12	22.80	4.31	10	1.29
S7BPLA	CGATGT GGG	17	13	24.91	3.21	8	1.18
S8BPLA	CTTGTA GGG	16	12	24.01	4.23	10	1.3
S9BPLA	GCCAAT GGG	26	22	27.23	5.58	14	1.5
S10BPLA	TGACCA GGG	24	20	23.89	3.76	11	1.29

^aSamples are formatted with the sample id (S#) followed by either BA (barcode absent) or BP (barcode present), and end with either LA (linker absent) or LP (linker present)
^bSequence from the template switching oligo present at the start of reads: barcodes are in bold, linker in italic, the 3G-tail is underlined
^cNumber of reads that map to unique genomic loci
^dPercent of reads that mapped to ribosomal RNA (rRNA)
^eCalculated as (number of uniquely mapped reads)/(number of unique read sequences)
^fCalculated as the number of protein coding genes with at least one transcription start site (TSS) peak (after G’-filtering)
^gCalculated as the average number of G’-filtered TSSs found per gene for genes in column ‘f’

ISSN: 1471-2164