Mercurial > repos > nikhil-joshi > deseq_and_sam2counts
comparison deseq/README.md @ 3:a49aff09553e draft default tip
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| author | nikhil-joshi |
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| date | Wed, 09 Jan 2013 18:39:12 -0500 |
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| 2:669899d20e59 | 3:a49aff09553e |
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| 1 # sam2counts and DESeq in Galaxy | |
| 2 | |
| 3 ## About | |
| 4 | |
| 5 This is a Galaxy package that wraps sam2counts and DESeq for RNA-Seq analysis using a transcriptome reference. sam2counts takes SAM or BAM files that are created from an alignment to a transcriptome and creates counts of aligned reads for each transcript. DESeq uses the DESeq package from Bioconductor in R and analyzes the count data from sam2counts. DESeq outputs a toptable of transcripts sorted by adjusted p-value and a page of diagnostic plots. | |
| 6 | |
| 7 ## Requirements | |
| 8 | |
| 9 Python 2.6.5 | |
| 10 pysam 0.6 (package for Python) | |
| 11 R 2.15 | |
| 12 Bioconductor 2.10 (package for R) | |
| 13 DESeq 1.8.3 (package for R) | |
| 14 aroma.light 1.24.0 (package for R) | |
| 15 lattice 0.20-6 (package for R) | |
| 16 | |
| 17 ## Installation | |
| 18 | |
| 19 stderr_wrapper.py and sam2counts_galaxy.py must be in the path or they can remain in the tools directory with the xml files. deseq.R must be copied to the "tool-data" directory under the main Galaxy install directory. | |
| 20 | |
| 21 ## Use | |
| 22 | |
| 23 sam2counts needs a SAM file (produced by aligning to a transcriptome) with header information as the input. The count data produced from this SAM file gets fed into DESeq. |