README
1 FX Tools
2 NGS Data Manipluation Tools
3
4 Version 0.2
5 August, 2013
6
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8Table of Contents
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10
11 1. Overview
12 2. Examples
13 3. Reference and Contact
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161. Overview
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202. Examples
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242.1 Help
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26
27You can get the manual for the tools by calling them with the --help command,
28for example:
29
30$ fx_bam_coverage --help
31
32prints the help of fx_bam_coverage.
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352.2 Coverage computation of SAM or BAM file
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37
38$ fx_bam_coverage
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413. Reference and Contact
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43
44Send an email to the SeqAn mailing list:
45
46 https://lists.fu-berlin.de/listinfo/seqan-dev
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494. R Snippets
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534.1. Conversion for Plotting with R
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55
56Converting the data.frame generated from the fx_fastq_stats TSV output into
57a list that can be plotted using bxp(R).
58
59 colnames(R) <- c("Column", "Count", "Minimal.Quality", "Maximal.Quality",
60 "Quality.Sum", "Quality.Mean", "1st.Quartile.Score",
61 "Median.Score", "3rd.Quartile.Score",
62 "Inter.Quality.Range", "Left.Whisker", "Right.Whisker",
63 "A.Count", "C.Count", "G.Count", "T.Count", "N.Count")
64 stats <- t(data.matrix(R[c("Minimal.Quality", "1st.Quartile.Score",
65 "3rd.Quartile.Score", "Maximal.Quality")]))
66 n <- R[, "Count"]
67 conf <- t(data.matrix(R[c("Minimal.Quality", "Maximal.Quality")]))
68 out <- c()
69 group <- c()
70 names <- c()
71 R <- list(stats=stats, n=n, conf=conf, out=out, group=group, names=names)
72