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author petr-novak
date Thu, 05 Sep 2019 09:04:56 -0400
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47 Tool for appending prefix and suffix to sequences names in fasta formated sequences. This tool is useful 47 Tool for appending prefix and suffix to sequences names in fasta formated sequences. This tool is useful
48 if you want to do comparative analysis with RepeatExplorer and need to 48 if you want to do comparative analysis with RepeatExplorer and need to
49 append sample codes to sequence identifiers 49 append sample codes to sequence identifiers
50 50
51 ### ChIP-Seq-mapper ###
52
53
54 Analysis of NGS sequences from Chromatin Imunoprecipitation. ChiP and Input reads are mapped to contigs obtained from graph based repetitive sequence clustering to enriched repeats. This method was used in (Neumann et al. 2012). for identification of repetitive sequences associated with cetromeric region.
55
56 #### Authors ####
57 Petr Novak, Jiri Macas, Pavel Neumann, Georg Hermanutz
58
59 Biology Centre CAS, Czech Republic
60
61
62 #### Installation and dependencies ####
63
64 ChIP-Seq-mapper require NCBI blast to be installed, R programming language with installed R2HTML and base64 packages and python3
65
66 #### Usage ####
67
68 ```
69 ChipSeqRatioAnalysis.py [-h] [-m MAX_CL] [-n NPROC] -c CHIPSEQ -i
70 INPUTSEQ [-o OUTPUT] [-ht HTML] [-t THRESHOLD]
71 -k CONTIGS
72
73 optional arguments:
74 -h, --help show this help message and exit
75 -m MAX_CL, --max_cl MAX_CL
76 Sets the maximum cluster number. Default = 200
77 -n NPROC, --nproc NPROC
78 Sets the number of cpus to be used. Default = all
79 available
80 -c CHIPSEQ, --ChipSeq CHIPSEQ
81 Fasta file containing the Chip Sequences
82 -i INPUTSEQ, --InputSeq INPUTSEQ
83 Fasta file containing the Input Sequences
84 -o OUTPUT, --output OUTPUT
85 Specify a name for the CSV file to which the output
86 will be save to. Default: ChipSeqRatio.csv
87 -ht HTML, --html HTML
88 Specify a name for the html report. Default :
89 ChipSeqRatioReport
90 -t THRESHOLD, --threshold THRESHOLD
91 Optional plot filter. Default: mean ration between
92 Input hits and Chip hits.
93 -k CONTIGS, --Contigs CONTIGS
94 Contig file for blast
95 ```
96
97 #### References ####
98 [PLoS Genet. Epub 2012 Jun 21. Stretching the rules: monocentric chromosomes with multiple centromere domains. Neumann P, Navrátilová A, Schroeder-Reiter E, Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J.](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777)
99
51 100
52 ## Dependencies ## 101 ## Dependencies ##
53 102
54 R programming environment with installed packages *optparse* and *ShortRead* (Bioconductor) 103 R programming environment with installed packages *optparse* and *ShortRead* (Bioconductor)
55 python3 104 python3