ncPRO-seq protocols

View ncPRO-seq computational protocol

ncPRO-seq statistics

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ncPRO-seq specifications

Information


Unique identifier OMICS_00366
Name ncPRO-seq
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ncPRO-seq

ncPRO-seq in pipelines

 (3)
2017
PMCID: 5477510
PMID: 28530238
DOI: 10.1038/ncomms15497

[…] in length, (3) adapter detection based on perfect 10-nucleotide match and (4) removal of reads without detected adapter. additionally, we used bowtie to align reads to the human genome (grch37) and ncpro-seq in combination with mirbase (v20) to match them to known mirna sequences. we used a detection threshold of 10 counts per mirna (present at least in 80% of libraries tested). a total of 281 […]

2017
PMCID: 5641107
PMID: 29069764
DOI: 10.18632/oncotarget.18270

[…] only trimmed reads with a length between 15 and 40 nucleotides were kept for the further analysis. data analysis was performed according to published pipeline ncpro-seq []. briefly, reads were mapped onto the hg19 genome assembly with bowtie v0.12.8 []. the annotations were done with mirbase release 20 for the micrornas, with repbase for the repeats […]

2014
PMCID: 4112208
PMID: 24997592
DOI: 10.1186/1471-2164-15-557

[…] been deposited in the geo database under the ncbi-geo accession number gse50396., sequence reads were processed using the casava1.8 pipeline (illumina). non-coding rna profiling was performed by the ncpro-seq analysis pipeline []. mirdeep2 analysis [] was employed to detect potential mirnas from raw rna sequencing data using default parameters. to quantify mir-71 associated sequence reads […]


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ncPRO-seq in publications

 (13)
PMCID: 5961502
PMID: 29035371
DOI: 10.1038/nm.4424

[…] shorter than 15 bp were excluded from the downstream analysis. reads were aligned to the human genome hg19 using bowtie. mapped reads were annotated, and mirna expression was quantified using ncpro-seq (version v1.5.1) based on mirbase v19. differentially expressed mirnas between cc-cr and cc cells were detected by edger. the p-values were adjusted by benjamini and hochberg's multiple […]

PMCID: 5641107
PMID: 29069764
DOI: 10.18632/oncotarget.18270

[…] only trimmed reads with a length between 15 and 40 nucleotides were kept for the further analysis. data analysis was performed according to published pipeline ncpro-seq []. briefly, reads were mapped onto the hg19 genome assembly with bowtie v0.12.8 []. the annotations were done with mirbase release 20 for the micrornas, with repbase for the repeats […]

PMCID: 5477510
PMID: 28530238
DOI: 10.1038/ncomms15497

[…] in length, (3) adapter detection based on perfect 10-nucleotide match and (4) removal of reads without detected adapter. additionally, we used bowtie to align reads to the human genome (grch37) and ncpro-seq in combination with mirbase (v20) to match them to known mirna sequences. we used a detection threshold of 10 counts per mirna (present at least in 80% of libraries tested). a total of 281 […]

PMCID: 5376654
PMID: 28332497
DOI: 10.1038/ncomms14852

[…] log2 ratio >0.5 and a p value <0.05. heatmaps and sample clustering are based on deseq2 normalized values. heatmaps display z-scores of normalized read counts., for the small rna experiment, ncpro-seq with default settings was used to quality control (qc), map and quantify the abundances of microrna. the average number of trimmed reads for small rna libraries was 11.5 million reads. […]

PMCID: 5435969
PMID: 28334969
DOI: 10.1093/nar/gkx119

[…] to the ncbi gene expression omnibus (geo) (gse89345)., small rna reads were filtered to 15–35nt long reads. reads with the same sequence were grouped using the processreads function from the ncpro-seq pipeline () and then matched against both the a. thaliana genome (tair10) and the transgenes (see ) using bowtie (). only reads with a maximum of one mismatch over their entire length […]


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ncPRO-seq institution(s)
Institut Curie, Paris, France

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