PIPE-CLIP protocols

View PIPE-CLIP computational protocol

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PIPE-CLIP specifications

Information


Unique identifier OMICS_02254
Name PIPE-CLIP
Interface Web user interface
Restrictions to use None
Input format SAM, BAM
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for PIPE-CLIP

PIPE-CLIP in pipelines

 (2)
2017
PMCID: 5663106
PMID: 29084609
DOI: 10.1186/s13059-017-1332-x

[…] identical reads including the same random barcode sequence were considered pcr duplicates and hence removed. the barcodes were trimmed from the remaining reads using barcoderemoval from pipe-clip []. the resulting reads were mapped to the a. thaliana tair10 reference genome with star v2.5.2a [] using the additional transcript annotation file atrtd.gff from atrtd, a novel reference […]

2016
PMCID: 4764554
PMID: 26744779
DOI: 10.7554/eLife.11155.029

[…] genome. basic parameters were the same as those previously described (): a maximum of two-nucleotide mismatches and a minimum of 25 high quality matches were allowed. bam files were then input into pipe-clip () to identify peaks with default parameters for iclip (upf1) and hits-clip (ptbp1). the peaks were annotated with pavis (), and homer () was used to quantify clip tag density around stop […]


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PIPE-CLIP in publications

 (9)
PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] is merely a result of transcript abundance or a more specific interaction between the rbp and its target rna. several peak calling programs have been developed and include piranha [], clipper [], pipe-clip [], pyicos [] that work with all clip variants, and paralyzer [] and wavcluster that are specifically developed for par-clip analysis. for more details on the statistical models underlying […]

PMCID: 5910864
PMID: 29610341
DOI: 10.1073/pnas.1722333115

[…] htseq (). genome-wide distribution of zc3h11a-hits-clip reads across the gene body was assessed using the read distribution tool of rseqc suite (). zc3h11a-specific filtered reads were submitted to pipe-clip () to define hits-clip peaks. top peaks were selected based on peak width for an uninfected sample cutoff of 150 nt (average peak width of 80 nt) and for an hadv-5–infected sample cutoff […]

PMCID: 5694010
PMID: 29150605
DOI: 10.1038/s41467-017-01613-1

[…] integrated genome viewer was used to visualize the alignments. duplicate reads were removed using picard markduplicates. the 3xflag-csra reads were merged into a single file and used as input into pipe-clip to identify clip-seq peaks. these peaks were used to count reads per peak with htseq count for each individual sample file. deseq2 was used to identify peaks significantly enriched […]

PMCID: 5187584
PMID: 28000671
DOI: 10.1038/ncomms13865

[…] in the 3′-utr of pafah1b1 to target, reads from the apc-clip study were collapse and quality-filtered and mapped to the mouse genome (mm10). mapped reads were analysed for cluster enrichment using pipe-clip. three clusters in the 3′-utr of pafah1b1 were found to be significantly enriched in apc-binding, but only two of these clusters had a significant fold change compared with a control […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] step is to find the precise cluster distribution profiles through enhancing the signal-to-noise ratio and decreasing the false-positive rate. data analysis methods developed for this purpose include pipe-clip, paralyzer, piranha, wavcluster, and dclip. the next downstream of the pipeline is the motif discovery, higher level structure prediction, and functional characterization. previously […]


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