Finite size effects in transcript sequencing count distribution

		Contact: Analytics of Biological Sequence Data Group Bioinformatics Institute

Supplementary materials to:

Finite size effects in transcript sequencing count distribution : its necessary power law correction and implications for downstream normalization and statistical analysis

Wing Cheong Wong, Hong kiat Ng, Erwin Tantoso, Richie Soong, Frank Eisenhaber

Dilution data set (in-house): NUGC3 (12p,6p,3p,1.5p) and AGS (12p,3p) cell lines

Below, we provide the Illumina miSeq RAW (Fastq) files of the dilution series

NUGC3 replicate 1 @ 12pM click here
NUGC3 replicate 2 @ 12pM click here
NUGC3 replicate 1 @ 6pM click here
NUGC3 replicate 2 @ 6pM click here
NUGC3 replicate 1 @ 3pM click here
NUGC3 replicate 2 @ 3pM click here
NUGC3 replicate 1 @ 1.5pM click here
NUGC3 replicate 2 @ 1.5pM click here
AGS replicate 1 @ 12pM click here
AGS replicate 2 @ 12pM click here
AGS replicate 1 @ 3pM click here
AGS replicate 2 @ 3pM click here

Below, we provide the summarized count data of the dilution series by different aligners (Bowtie1, Bowtie2(global), Novoalign, BWA)

Bowtie1-mapped 865 NUGC3-only(12p,6p,3p,1.5p) transcript counts click here
Bowtie1-mapped 1009 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts click here
Bowtie1-mapped 637 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts with removal of NUGC3 or AGS zero-count click here
Bowtie2(global)-mapped 1061 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts click here
Bowtie2(global)-mapped 657 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts with removal of NUGC3 or AGS zero-count click here
Novoalign-mapped 1090 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts click here
Novoalign-mapped 673 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts with removal of NUGC3 or AGS zero-count click here
BWA-mapped 1083 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts click here
BWA-mapped 670 NUGC3(12p,6p,3p,1.5p)+AGS(12p,3p) transcript counts with removal of NUGC3 or AGS zero-count click here

Spike-in data set (public GSE67074) : 12 spike-in transcripts and UHR (Universal Human reference as background)

Below, we provide the summarized count data of the dilution series by different aligners (Bowtie1, Bowtie2(global), BWA, Novoalign)

BWA-mapped 1387 UHR-only transcripts click here
BWA-mapped 460 UHR-only transcripts with removal of zero-count across 12 replicates click here
BWA-mapped 12 spike-in transcripts click here

Power-law correction perl program

Below, we provide the program (written as PERL modules) that performs the power-law correction on the sequencing data.

download the program here

All files are compressed by WinRAR