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Table 1 Summary of sequencing and alignment results

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

Samplesa Adaptor Sequenceb Number of Raw Reads (×106) Uniquely Mapped Readsc (×106) % rRNA Readsd Redundancye Average # of Genes with TSS Peaks (×103)f Average # of Peaks per Geneg
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
  1. 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)
  2. bSequence from the template switching oligo present at the start of reads: barcodes are in bold, linker in italic, the 3G-tail is underlined
  3. cNumber of reads that map to unique genomic loci
  4. dPercent of reads that mapped to ribosomal RNA (rRNA)
  5. eCalculated as (number of uniquely mapped reads)/(number of unique read sequences)
  6. fCalculated as the number of protein coding genes with at least one transcription start site (TSS) peak (after G’-filtering)
  7. gCalculated as the average number of G’-filtered TSSs found per gene for genes in column ‘f’