ReferenceAnnotationDownload modified by J.Herstein

J.Herstein — Fri, 31 Jan 2014 20:36:38 -0000
--- v1
+++ v2
@@ -1,52 +1,46 @@
-We collected the required annotation files for `RseqFlow` running of six model species. 
-
-  * Human-Homo Sapiens
-  * Mouse-Mus musculus
-  * Rhesus-Macaca Mulatta
-  * c.elegans
-  * Fruitfly-drosophila melanogaster
-  * yeast-S.cerevisiae
+RseqFlow required annotation files:
+[TOC]

 # Human-Homo Sapiens

->   * [Genome Annotation File (GTF format) (GencodeV14)](http://code.google.com/p/rseqflow/downloads/detail?name=Human_gencodeV14_anno.gtf.gz&can=2&q=)
-  * [Transcriptome reference sequences (GencodeV14)](http://code.google.com/p/rseqflow/downloads/detail?name=Human_gencodeV14_transcripts.fa.gz&can=2&q=)
+  * [Genome Annotation File (GTF format) (GencodeV14)](http://sourceforge.net/projects/rseqflow/files/Human_gencodeV14_anno.gtf.gz/download)
+  * [Transcriptome reference sequences (GencodeV14)](http://sourceforge.net/projects/rseqflow/files/Human_gencodeV14_transcripts.fa.gz/download)
   * [Genome reference sequences (Ensembl V69 GRch37/Hg19)](http://genomics.isi.edu/downloads/Human_genome_GRCh37_69.fa.gz)
-  * [Mitochondria reference sequence](http://code.google.com/p/rseqflow/downloads/detail?name=Human_chrM.fa&can=2&q=)
-  * [Ribosomal RNA reference sequences](http://code.google.com/p/rseqflow/downloads/detail?name=human_all_rRNA.fasta&can=2&q=)
+  * [Mitochondria reference sequence](http://sourceforge.net/projects/rseqflow/files/Human_chrM.fa/download)
+  * [Ribosomal RNA reference sequences](http://sourceforge.net/projects/rseqflow/files/human_all_rRNA.fasta/download)

 # Mouse-Mus musculus

-  * [Genome Annotation File (GTF format) from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=mouse_refseq_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=mouse_refseq_seq.fa&can=2&q=)
-  * [Genome Annotation File (GTF format) from Ensembl](http://code.google.com/p/rseqflow/downloads/detail?name=mouse_ensembl_anno.gtf.gz&can=2&q=)
-  * [Reference Transcriptome Sequences from Ensembl](http://code.google.com/p/rseqflow/downloads/detail?name=mouse_ensembl_seq.fa&can=2&q=)
+  * [Genome Annotation File (GTF format) from RefSeq](http://sourceforge.net/projects/rseqflow/files/mouse_refseq_anno.gtf/download)
+  * [Reference Transcriptome Sequences from RefSeq](http://sourceforge.net/projects/rseqflow/files/mouse_refseq_seq.fa/download)
+  * [Genome Annotation File (GTF format) from Ensembl](http://sourceforge.net/projects/rseqflow/files/mouse_ensembl_anno.gtf.gz/download)
+  * [Reference Transcriptome Sequences from Ensembl](http://sourceforge.net/projects/rseqflow/files/mouse_ensembl_seq.fa/download)
   * [Genome Sequence(GRCm38/mm10)](http://genomics.isi.edu/downloads/genome_mouse.fa.gz)

 # Rhesus-Macaca Mulatta

-  * [Genome Annotation File (GTF format) from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=rhesus_refseq_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=rhesus_refseq_seq.fa&can=2&q=)
+  * [Genome Annotation File (GTF format) from RefSeq](http://sourceforge.net/projects/rseqflow/files/rhesus_refseq_anno.gtf/download)
+  * [Reference Transcriptome Sequences from RefSeq](http://sourceforge.net/projects/rseqflow/files/rhesus_refseq_seq.fa/download)
   * [Genome Sequence(MGSC Merged/rheMac2)](http://genomics.isi.edu/downloads/rhesus_genome.fa.gz)

 # c.elegans

-  * [Genome Annotation File (GTF format) from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=c.elegans_refseq_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=c.elegans_refseq_seq.fa&can=2&q=)
-  * [Genome Sequence(WS220/ce10)](http://code.google.com/p/rseqflow/downloads/detail?name=genome_c.elegans.fa.gz&can=2&q=)
+  * [Genome Annotation File (GTF format) from RefSeq](http://sourceforge.net/projects/rseqflow/files/c.elegans_refseq_anno.gtf/download)
+  * [Reference Transcriptome Sequences from RefSeq](http://sourceforge.net/projects/rseqflow/files/c.elegans_refseq_seq.fa/download)
+  * [Genome Sequence(WS220/ce10)](http://sourceforge.net/projects/rseqflow/files/genome_c.elegans.fa.gz/download)

 # Fruitfly-drosophila melanogaster

-  * [Genome Annotation File (GTF format) from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=fruitfly_refseq_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from RefSeq](http://code.google.com/p/rseqflow/downloads/detail?name=fruitfly_refseq_seq.fa&can=2&q=)
-  * [Genome Annotation File (GTF format) from Ensembl](http://code.google.com/p/rseqflow/downloads/detail?name=fruitfly_ensembl_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from Ensembl](http://code.google.com/p/rseqflow/downloads/detail?name=fruitfly_ensembl_seq.fa&can=2&q=)
-  * [Genome Sequence(BDGP R5/dm3)](http://code.google.com/p/rseqflow/downloads/detail?name=genome_fruitfly.fa.gz&can=2&q=)
+  * [Genome Annotation File (GTF format) from RefSeq](http://sourceforge.net/projects/rseqflow/files/fruitfly_refseq_anno.gtf/download)
+  * [Reference Transcriptome Sequences from RefSeq](http://sourceforge.net/projects/rseqflow/files/fruitfly_refseq_seq.fa/download)
+  * [Genome Annotation File (GTF format) from Ensembl](http://sourceforge.net/projects/rseqflow/files/fruitfly_ensembl_anno.gtf/download)
+  * [Reference Transcriptome Sequences from Ensembl](http://sourceforge.net/projects/rseqflow/files/fruitfly_ensembl_seq.fa/download)
+  * [Genome Sequence(BDGP R5/dm3)](http://sourceforge.net/projects/rseqflow/files/genome_fruitfly.fa.gz/download)

 # yeast-S.cerevisiae

-  * [Genome Annotation File (GTF format) from SGD](http://code.google.com/p/rseqflow/downloads/detail?name=yeast_SGD_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from SGD](http://code.google.com/p/rseqflow/downloads/detail?name=yeast_SGD_seq.fa&can=2&q=)
-  * [Genome Annotation File (GTF format) from Ensembl](http://code.google.com/p/rseqflow/downloads/detail?name=yeast_ens_anno.gtf&can=2&q=)
-  * [Reference Transcriptome Sequences from Ensembl](http://code.google.com/p/rseqflow/downloads/detail?name=yeast_ens_seq.fa&can=2&q=)
-  * [Genome Sequence(sacCer3)](http://code.google.com/p/rseqflow/downloads/detail?name=genome_yeast.fa.gz&can=2&q=)
+  * [Genome Annotation File (GTF format) from SGD](http://sourceforge.net/projects/rseqflow/files/yeast_SGD_anno.gtf/download)
+  * [Reference Transcriptome Sequences from SGD](http://sourceforge.net/projects/rseqflow/files/yeast_SGD_seq.fa/download)
+  * [Genome Annotation File (GTF format) from Ensembl](http://sourceforge.net/projects/rseqflow/files/yeast_ens_anno.gtf/download)
+  * [Reference Transcriptome Sequences from Ensembl](http://sourceforge.net/projects/rseqflow/files/yeast_ens_seq.fa/download)
+  * [Genome Sequence(sacCer3)](http://sourceforge.net/projects/rseqflow/files/genome_yeast.fa.gz/download)
Recent changes to ReferenceAnnotationDownload

ReferenceAnnotationDownload modified by J.Herstein

RseqFlow required annotation files:

ReferenceAnnotationDownload modified by Anonymous

Human-Homo Sapiens

Mouse-Mus musculus

Rhesus-Macaca Mulatta

c.elegans

Fruitfly-drosophila melanogaster

yeast-S.cerevisiae
