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    New releases and related tools will be announced through the mailing list

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    Questions about Cufflinks and Cuffdiff should be posted on our Google Group. Please use tophat.cufflinks@gmail.com for private communications only. Please do not email technical questions to Cufflinks contributors directly.

Releases

Related Tools

  • Monocle: Single-cell RNA-Seq analysis
  • CummeRbund: Visualization of RNA-Seq differential analysis
  • TopHat: Alignment of short RNA-Seq reads
  • Bowtie: Ultrafast short read alignment

Publications

Contributors

Links

Illumina has provided the RNA-Seq user community with a set of genome sequence indexes (including Bowtie indexes) as well as GTF transcript annotation files. These files can be used with TopHat and Cufflinks to quickly perform expression analysis and gene discovery. The annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis. We recommend that you download your Bowtie indexes and annotation files from this page. More information about Illumina's iGenomes project can be found here.

Organism Data source Version Size Last Modified
Homo sapiens Ensembl GRCh37 17297 MB May 14 17:23
NCBI build36.3 15814 MB May 14 19:36
build37.1 15850 MB May 14 19:04
build37.2 21450 MB May 14 17:54
UCSC hg18 17349 MB May 14 15:31
hg19 21058 MB May 14 15:36
Mus musculus Ensembl NCBIM37 14428 MB May 14 22:13
NCBI build37.1 15260 MB May 15 17:53
build37.2 15725 MB May 14 22:52
UCSC mm9 14537 MB May 14 21:12
mm10 14193 MB Jun 14 11:29
Rattus norvegicus Ensembl RGSC3.4 13725 MB May 15 22:33
NCBI RGSC_v3.4 14234 MB May 15 23:58
UCSC rn4 13710 MB May 15 22:32
Bos taurus Ensembl Btau_4.0 13315 MB May 11 14:18
UMD3.1 14042 MB May 11 12:41
NCBI Btau_4.2 13357 MB May 11 14:11
Btau_4.6.1 13448 MB May 11 16:09
UMD_3.1 13990 MB May 11 16:08
UCSC bosTau4 13386 MB May 11 12:36
Canis familiaris Ensembl BROADD2 13087 MB May 11 18:00
NCBI build2.1 12847 MB May 11 19:22
build3.1 12528 MB May 11 19:30
UCSC canFam2 13138 MB May 11 17:50
Gallus gallus Ensembl WASHUC2 5547 MB May 14 12:30
NCBI build2.1 5592 MB May 14 13:08
build3.1 5469 MB May 14 13:18
UCSC galGal3 5546 MB May 14 11:52
Drosophila melanogaster Ensembl BDGP5 669 MB May 11 19:35
BDGP5.25 692 MB May 11 19:32
NCBI build4.1 701 MB May 11 19:38
build5 701 MB May 11 19:41
build5.3 674 MB May 11 19:40
UCSC dm3 763 MB May 11 19:28
Arabidopsis thaliana Ensembl TAIR9 710 MB May 11 10:47
TAIR10 679 MB May 11 10:46
NCBI build9.1 721 MB May 11 10:51
TAIR10 658 MB May 11 10:51
Caenorhabditis elegans Ensembl WS210 597 MB May 11 16:16
WS220 560 MB May 11 16:17
NCBI WS190 566 MB May 11 16:21
WS195 554 MB May 11 16:21
UCSC ce6 617 MB May 11 16:13
ce10 552 MB May 11 16:12
Saccharomyces cerevisiae Ensembl EF2 74 MB May 15 22:35
EF3 72 MB May 15 22:35
EF4 71 MB May 15 22:34
NCBI build2.1 70 MB May 15 22:36
build3.1 70 MB May 15 22:36
UCSC sacCer2 70 MB May 15 22:34
sacCer3 70 MB May 15 22:33