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P000001125

nAnT-iCAGE


Introduction


A mapping pipeline for nAnT-iCAGE protocol. bwa is used for mapping. When barcode information is empty, extraction step will be skipped. This pipeline can't handle library with mixed genome.


Input formatFASTQ(Illumina, etc...)
Library layoutFor single-end read only
SpeciesHuman(hg19), Mouse(mm9), Rat(rn4), Chicken(galGal3), Dog(canFam2)
Execution timeAbout 22 hours (30M single-end reads[54bp])



Results
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CTSS results(BED format)
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Genome Explorer
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Mapping report


Workflow
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Inputs


FASTQ-formatted dna sequence file (single-end)

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read sequence

FASTQ Format Specification(external link)

Outputs


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CTSS results(BED format)
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Genome Explorer

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Mapping report
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Mapping report(remove PCR duplication)

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raw base distribution
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base N distribution
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rRNA base distribution


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no barcode sequence top100
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rRNA sequence top100
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mapped sequence top100
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unmapped sequence top100

Options





Use case








Public
#Tool nameLink to original siteLink to our wiki site
1BWA(Original site)(external link)(NGS Surfer's wiki)(external link)
2SAMtools(Original site)(external link)(NGS Surfer's wiki)(external link)
3SAMstat(Original site)(external link)


Private
#Script name
1baseSeq(RIKEN CLST)
2Graph.sh(RIKEN CLST)
3splitByBarcode(RIKEN CLST)
4sampleTopSeq(RIKEN CLST)
5removeN(RIKEN CLST)
6rRNAdust(RIKEN CLST)
7bam_to_ctssbed.sh(RIKEN CLST)