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Request ID: DP00070600 Status: End
Pipeline ID: P000001539 Request Date: 2014/06/05 16:24
Pipeline Name: nAnT-iCAGE (RIKEN CLST) v1.1 Start Date: 2014/06/05 16:25
Pipeline Summary: A mapping pipeline for nAnT-iCAGE protocol. bwa is used for mapping. When barcode information is empty, extraction step will be skipped. This pipeline is for users outside OMICS or library information doesn End Date: 2014/06/05 16:56
Input Dataset:
K562CellRep1.ext(DS00265226)
Output Dataset:
(DS00265355)

rRNA(DS00265353)

Raw(DS00265322)

rRNA redundancy(DS00265349)

rRNA(DS00265347)

without N(DS00265335)

bam_to_ctssbed

sampleTopSeq [i...

samtools view (...
fastq (single-end)
K562CellRe... (DS00265226)
other
rRNA (DS00265347)
other
rRNA redun... (DS00265349)
fastq (single-end)
no rRNA (DS00265340)
fastq (single-end)
rRNA (DS00265341)

sampleTopSeq [i...

sampleTopSeq [i...

BWA (SE)

base N distribu...

SAMStat

loadBAM2ge_db (...

SAMStat

Remove PCR dupl...

sampleTopSeq [i...

rRNAdust
fastq (single-end)
Trimmed (DS00265333)
html
(DS00265377)
fastq (single-end)
without N (DS00265335)
fastq (single-end)
with N (DS00265336)
html
with N (DS00265338)

base N distribu...
other
unmapped (DS00265371)
bam
mapped (DS00265373)
fastq (single-end)
Filtered (DS00265331)
other
mapped (DS00265375)

splitByBarcode

raw base distri...

grepSeq (single...

sampleTopSeq [i...

removeN

fastx_trimmer (...
other
no barcode (DS00265329)
html
Raw (DS00265322)
html
rmdup (DS00265365)
fastq (single-end)
with barco... (DS00265324)
bed
ctss (DS00265367)
bam
unmapped (DS00265369)
fastq (single-end)
no barcode (DS00265325)
bam
rmdup (DS00265363)
bam
(DS00265355)

(DS00265357)
html
(DS00265359)
other
rRNA (DS00265351)
html
rRNA (DS00265353)

sampleTopSeq [i...

samtools view (...

nAnT-iCAGE: pri...