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comparison ChipSeqRatioDef.xml @ 9:c2c69c6090f0 draft

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author petr-novak
date Fri, 31 Jan 2020 06:55:23 -0500
parents 89c5ba120b21
children 5376e1c9adec
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8:99569eccc583 9:c2c69c6090f0
20 --bitscore=$bitscore 20 --bitscore=$bitscore
21 --nproc=16 21 --nproc=16
22 </command> 22 </command>
23 23
24 <inputs> 24 <inputs>
25 <param name="ChipFile" label="Chip Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 25 <param name="ChipFile" label="Chip reads" type="data" format="fasta" help="Reads in FASTA format"/>
26 <param name="InputFile" label="Input Sequences" type="data" format="fasta" help="NGS data in fasta format"/> 26 <param name="InputFile" label="Input reads" type="data" format="fasta" help="Reads in FASTA format"/>
27 <param name="ContigFile" label="Reference - Contig Sequences" type="data" format="fasta" 27 <param name="ContigFile" label="Reference - contig sequences" type="data" format="fasta"
28 help="Contigs obtained from RepeatExplorer clustering pipeline in fasta file"/> 28 help="Contigs from RepeatExplorer clustering (the file &quot;contigs.fasta&quot;)"/>
29 <param name="MaxCl" label="Number of clusters to be shown in graph" type="integer" value="200"/> 29 <param name="MaxCl" label="Number of top clusters to be shown in graph" type="integer" value="200"/>
30 <param name="bitscore" label="Minimum bit score threshold" type="integer" value="50" help="All similarity hits with lower bit score will not be considered for ChIP/Input ratio calculation"/> 30 <param name="bitscore" label="Bit score threshold" type="integer" value="50" help="Similarity hits with lower bit score will not be used for ChIP/Input ratio calculation"/>
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>
33 <data name="OutputFile" format="tabular" 33 <data name="OutputFile" format="tabular"
34 label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> 34 label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>
35 35
38 </outputs> 38 </outputs>
39 39
40 <help> 40 <help>
41 **What it does** 41 **What it does**
42 42
43 Analysis of NGS sequences from Chromatin Imunoprecipitation. ChiP 43 The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing data from chromatin
44 and Input reads are mapped to contigs obtained from graph based 44 immunoprecipitation experiments, using repeats identified by RepeatExplorer as the reference. The tool
45 repetitive sequence clustering(`Novak et al. 2013`__) to enriched repeats. Reads from input 45 performs BLASTN similarity search of the read sequences to the reference,
46 and ChIP should be ideally short illumina reads with uniform length 46 and the reads producing hits that passed the user-specified similarity threshold are assigned to the
47 above 80 nt. It is sufficiant to use about 1 milion of reads for both Input and Chip. 47 repeat clusters. The assignment is made to the cluster that produced the best similarity hit, and every
48 read is assigned to only a single cluster. Following read mapping, the numbers of reads from the
49 INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read counts are reported
50 for individual clusters.
51 ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score threshold value should be
52 adjusted based on the length of the analyzed reads (the value equal to the read length is recommended for a start).
48 This method was first used in (`Neumann et al. 2012`__) for 53 This method was first used in (`Neumann et al. 2012`__) for
49 identification of repetitive sequences associated with cetromeric 54 identification of repetitive sequences associated with centromeres:
50 region. If you use this method, reference:
51 55
52 56
53 `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.`__. 57 `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.`__.
54 58
55 .. __: http://bioinformatics.oxfordjournals.org/content/29/6/792.full
56
57 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 59 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
58 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 60 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
59 61
60 </help> 62 </help>
61 63