NEUMA

Normalization by Expected Uniquely Mappable Area

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

Soohyun Lee, Chae Hwa Seo, Byungho Lim, Jin Ok Yang, Jeongsu Oh, Minjin Kim, Sooncheol Lee, Byungwook Lee, Changwon Kang, Sanghyuk Lee
Nucl. Acids Res. (2010) doi: 10.1093/nar/gkq1015

News

Usage format is now more flexible. Multi-threading option for bowtie is added. Better error handling. 4/28/2011

mm9 75bp Ensembl GRCh37.61 single-end tables and hg19 RefSeq 50bp,100bp paired-end tables are now available. 4/10/2011

NEUMA 1.0.5 Release 4/5/2011

* This version fixed a bug in reading mapping stat file in the Ensembl mode.

mm9 72bp paired-end tables and 41bp single-end tables are ready. 2/14/2011

mm9 36bp paired-end tables and Ensembl GRCh37.58 (H.sapiens) paired-end 75bp tables are ready. 12/31/2010

hg19,mm9 and dmel-5.25 single-end 100bp tables are ready. 12/27/2010

Ensembl GRCh37.58 (H.sapiens) paired-end 36bp tables and mm9 RefSeq paired-end 50bp & 75bp tables are ready. 12/27/2010

75bp and 78bp paired-end tables are ready for hg19 RefSeq. 12/24/2010

Single-end tables for dmel-5.25 (Ensembl 60) is ready. 12/18/2010

mm9 RefSeq single-end tables are now available. 12/13/2010

hg19 RefSeq data and single-end tables are updated. 12/13/2010

* Minor bug fixes such as double-counting of reads whose reverse complementary sequence exists on the same transcript.

* gene2NM and refMrna.fa are now perfectly matched, by removal of some obsolete NM numbers and addition of new genes.

NEUMA 1.0.4 Release 11/30/2010

* NEUMA can handle Ensembl data.

50bp single-end preprocessing tables are now available for hg19 RefSeq.

NEUMA 1.0.3 Release 11/23/2010

* The new version handles SOLiD colorspace data.

NEUMA 1.0.2 Release 10/8/2010

* The codes became neater.
* A small change of intermediate file formats.
* A script for preliminary runs (to determine sample insert length distribution) is added

NEUMA 1.0.1 Release 8/13/2010


Download

NEUMA package (v1.1.0)  README
NEUMA package (v1.0.5)  
Bowtie can be obtained from here.

Sample RNA-Seq data

gU & iU tables

== RefSeq ==


hg19 RefSeq (same for hg18)

gene2MN / gene2Symbol / RefSeq fasta /
bowtie reference index file for Illumina data(bowtie-0.12.7) / bowtie reference index file for SOLiD data(bowtie-0.12.7)

♦ Paired-end
Read length insert size gUd,g iUd,i
36bp 37-250 gU file iU file
50bp 51-400 gU file iU file
75bp 76-400 gU file iU file
78bp 79-600 gU file iU file
100bp 101-300 gU file iU file
♦ Single-end
Read length gEUMA iEUMA
32bp gEUMA file iEUMA file
36bp gEUMA file iEUMA file
50bp gEUMA file iEUMA file
75bp gEUMA file iEUMA file
100bp gEUMA file iEUMA file

mm9 RefSeq (same for mm8)

gene2MN / gene2Symbol / RefSeq fasta /
bowtie reference index file for Illumina data(bowtie-0.12.7) / bowtie reference index file for SOLiD data(bowtie-0.12.7)

♦ Paired-end
Read length insert size gUd,g iUd,i
36bp 37-250 gU file iU file
50bp 51-400 gU file iU file
72bp 73-1072 gU file iU file
75bp 76-500 gU file iU file
♦ Single-end
Read length gEUMA iEUMA
36bp gEUMA file iEUMA file
40bp gEUMA file iEUMA file
41bp gEUMA file iEUMA file
50bp gEUMA file iEUMA file
75bp gEUMA file iEUMA file
100bp gEUMA file iEUMA file


== Ensembl ==


H.sapiens (GRCh37.58)

ENSG2ENST / ENSG2Symbol / Ensembl RNA(cDNA+ncRNA) /
bowtie reference index file for Illumina data(bowtie-0.12.7) / bowtie reference index file for SOLiD data(bowtie-0.12.7)

♦ Paired-end
Read length insert size gUd,g iUd,i
36bp 37-248 gU file iU file
50bp 51-400 gU file iU file
75bp 76-400 gU file iU file
♦ Single-end
Read length gEUMA iEUMA
50bp gEUMA file iEUMA file

D.melanogaster 5.25 (Ensembl 60)

ENSG2ENST / ENSG2Symbol / Ensembl RNA(cDNA) /
bowtie reference index file for Illumina data(bowtie-0.12.7) / bowtie reference index file for SOLiD data(bowtie-0.12.7)

♦ Paired-end
Read length insert size gUd,g iUd,i
76bp 77-400 gU file iU file
♦ Single-end
Read length gEUMA iEUMA
100bp gEUMA file iEUMA file

Mus Musculus NCBIM37 (Ensembl 61)

ENSG2ENST / ENSG2Symbol / Ensembl RNA(cDNA+ncRNA) /
bowtie reference index file for Illumina data(bowtie-0.12.7) / bowtie reference index file for SOLiD data(bowtie-0.12.7)

♦ Single-end
Read length gUd,g iUd,i
75bp gU file iU file


If you need the pre-processed tables (gU & iU) for other transcriptome or for different experimental setup, please request through this link.

In case you experience any inconvenience or problem requesting U tables, please do not hesitate and drop us an email! :)

WEBMASTER chseo at kribb.re.kr mail_to
NEUMA duplexa at gmail.com mail_to