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rseqflow2-v2.2.tar.gz (29.8 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| README | 2014-09-21 | 2.5 kB | |
| rseqflow2-v2.2.tar.gz | 2014-09-21 | 29.8 MB | |
| rseqflow2-v2.1.tar.gz | 2013-12-04 | 29.8 MB | |
| rseqflow2-v2.0.tar.gz | 2013-09-13 | 59.1 MB | |
| ERR030893_2M.fastq.gz | 2013-09-12 | 122.4 MB | |
| Human_chrM.fa | 2013-09-10 | 16.9 kB | |
| Human_gencodeV14_transcripts.fa.gz | 2013-09-10 | 43.5 MB | |
| Human_gencodeV14_anno.gtf.gz | 2013-09-10 | 15.2 MB | |
| SRR514378.fastq.gz | 2012-09-11 | 103.9 MB | |
| supplementary-RseqFlow-formalpublish.doc | 2012-09-10 | 1.6 MB | |
| RseqFlow-formalPublish.pdf | 2012-09-10 | 75.5 kB | |
| chrM_human.fa | 2012-09-07 | 16.9 kB | |
| genome_yeast.fa.gz | 2012-09-07 | 3.8 MB | |
| genome_fruitfly.fa.gz | 2012-09-07 | 51.4 MB | |
| genome_c.elegans.fa.gz | 2012-09-07 | 31.8 MB | |
| yeast_ens_anno.gtf | 2012-09-07 | 4.1 MB | |
| yeast_SGD_anno.gtf | 2012-09-07 | 4.1 MB | |
| yeast_ens_seq.fa | 2012-09-07 | 10.0 MB | |
| yeast_SGD_seq.fa | 2012-09-07 | 9.8 MB | |
| rhesus_refseq_seq.fa | 2012-09-07 | 71.8 MB | |
| mouse_ensembl_seq.fa | 2012-09-07 | 187.5 MB | |
| mouse_ensembl_anno.gtf.gz | 2012-09-07 | 14.5 MB | |
| mouse_refseq_seq.fa | 2012-09-07 | 89.6 MB | |
| mouse_refseq_anno.gtf | 2012-09-07 | 90.8 MB | |
| human_all_rRNA.fasta | 2012-09-07 | 10.3 kB | |
| Human_gencodeV12_seq.fa.gz | 2012-09-07 | 44.6 MB | |
| Human_gencodeV12_anno.gtf.gz | 2012-09-07 | 16.1 MB | |
| fruitfly_ensembl_seq.fa | 2012-09-07 | 57.6 MB | |
| fruitfly_ensembl_anno.gtf | 2012-09-07 | 44.1 MB | |
| fruitfly_refseq_seq.fa | 2012-09-07 | 69.0 MB | |
| fruitfly_refseq_anno.gtf | 2012-09-07 | 47.8 MB | |
| rhesus_refseq_anno.gtf | 2012-09-07 | 93.8 MB | |
| c.elegans_refseq_anno.gtf | 2012-09-07 | 63.1 MB | |
| c.elegans_refseq_seq.fa | 2012-09-07 | 41.4 MB | |
| Totals: 34 Items | 1.5 GB | 0 |
***************************** *** Version Release Notes *** ***************************** *** Version 2.2 - 2014 September 22 *** - Create a combined QC pdf report if user has ImageMagick installed. *** Version 2.1 - 2013 December 04 *** - Expression Estimation now uses only unique alignments rather than "best" alignment. - Replaced deprecated function in DE branch. *** Version 2.0 - 2013 September 10 *** - This is a smaller version of the original `RseqFlow` that has been implemented to run on a 4G or larger laptop or desktop machine. - In the interest of speed and memory usage, Bowtie2 is now the only alignment tool. Perm and BWA are not supported at this time. - Only the single "best" mapped reads are used for analysis, multi-mapped options are no longer offered. - The "DE.sh image" function is not supported in this version. **************** *** Citation *** **************** Please cite our publication in the Bioinformatics journal: Ying Wang, Gaurang Mehta, Rajiv Mayani, Tade Souaiaia, Yangho Chen, Andrew Clark, Lin Wan, Oleg V. Evgrafov, James A. Knowles, Ewa Deelman and Ting Chen, RseqFlow: workflows for RNA-Seq data analysis. Bioinformatics, 2011, 27 (18): 2598–2600_. ([http://sourceforge.net/projects/rseqflow/files/RseqFlow-formalpublish.doc/download), (http://sourceforge.net/projects/rseqflow/files/supplementary-RseqFlow-formalpublish.doc/download) ***************** *** Downloads *** ***************** - The source code for the Unix package can be downloaded from: http://sourceforge.net/projects/rseqflow/files/rseqflow2-v2.1.tar.gz/download - Information for the Pegasus workflow version is here: http://genomics.isi.edu/rnaseq - The required reference annotation files for several model species can be downloaded from here: https://sourceforge.net/p/rseqflow/wiki/ReferenceAnnotationDownload ************************ *** Development Team *** ************************ The source code and Unix run mode of `RseqFlow` was developed by Ting Chen's group, Computational Molecular Biology, University of Southern California and Ying Wang's group, Automation Department, Xiamen University. The VM workflow run mode was constructed by Ewa Deelman's group at Information Sciences Institute, University of Southern California. The source code is maintained by James Knowles' group at Keck School of Medicine, University of Southern California. All suggestions are welcome, please email DL-RSEQFLOW-QUESTIONS@med.usc.edu