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1 # sam2counts and DESeq in Galaxy
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2
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3 ## About
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4
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5 This is a Galaxy package that wraps sam2counts and DESeq for RNA-Seq analysis using a transcriptome reference. sam2counts takes SAM 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.
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6
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7 ## Requirements
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8
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9 Python 2.6.5
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10 pysam 0.6 (package for Python)
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11 R 2.15
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12 Bioconductor 2.10 (package for R)
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13 DESeq 1.8.3 (package for R)
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14 aroma.light 1.24.0 (package for R)
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15 lattice 0.20-6 (package for R)
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16
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17 ## Installation
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18
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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.
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21 ## Use
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22
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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.
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