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PIPE-CLIP specifications


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


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Publication for PIPE-CLIP

PIPE-CLIP citations


CLIP related methodologies and their application to retrovirology

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

[…] ent 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 t […]


Multiple nuclear replicating viruses require the stress induced protein ZC3H11A for efficient growth

Proc Natl Acad Sci U S A
PMCID: 5910864
PMID: 29610341
DOI: 10.1073/pnas.1722333115

[…] g 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 of […]


Review: Electrostatically actuated nanobeam based nanoelectromechanical switches – materials solutions and operational conditions

Beilstein J Nanotechnol
PMCID: 5789396
PMID: 29441272
DOI: 10.3762/bjnano.9.29

[…] a TiW switching element and W as the contact electrode []. A jump-in voltage lower than 1 V and on/off current ratio higher than 105 were demonstrated for this 2T NEM switch, employing an innovative “pipe-clip” architecture. However, the device showed poor reliability with marked deterioration in performance after 10–20 switching cycles. This was attributed to physical degradation of contacts, as […]


Global role of the bacterial post transcriptional regulator CsrA revealed by integrated transcriptomics

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

[…] e. 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 (adjusted […]


Adaptation of iCLIP to plants determines the binding landscape of the clock regulated RNA binding protein AtGRP7

Genome Biol
PMCID: 5663106
PMID: 29084609
DOI: 10.1186/s13059-017-1332-x

[…] sseLab/iCLIP. 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 tr […]


Local synthesis of dynein cofactors matches retrograde transport to acutely changing demands

Nat Commun
PMCID: 5187584
PMID: 28000671
DOI: 10.1038/ncomms13865

[…] fs 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 mRNA-se […]


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