MiClip protocols

View MiClip computational protocol

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MiClip specifications

Information


Unique identifier OMICS_06672
Name MiClip
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for MiClip

MiClip in pipelines

 (4)
2017
PMCID: 5500889
PMID: 28675155
DOI: 10.1038/ncomms15737

[…] with the cims software package using the following awk command: awk -f ‘[_/]’ ‘/ˆ>/{print $1‘_’$2‘_’$3‘/’$4‘#’$3‘#’$2; getline($9); print $9}’. paired-end rna-seq data from control mrna and miclip for six embryo developmental timepoints were mapped to the drosophila reference genome sequence (version r5.45) with subread-align package from the subread software suite. read counts […]

2017
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] complexes were processed by crosslinking, immunoprecipitation, rna 3′ linker ligation, purification, and reverse transcription exactly as previously described., after sequencing, we used the miclip pipeline as previously described. in summary, raw miclip reads were trimmed of their 3′ adaptor and demultiplexed. then, pcr-duplicated reads of identical sequences were removed using […]

2015
PMCID: 4477666
PMID: 25958398
DOI: 10.1093/nar/gkv439

[…] i.e. the dependency is in the hidden states. this structure enables the hmm to incorporate the spatial dependency of the genome-wide clip data. among the tools developed for clip data, dclip and miclip used hmm while also accounting for the other special properties of the genome-wide clip data and they have been shown to improve the identification of rbp-binding targets or differential […]

2015
PMCID: 4487409
PMID: 26121403
DOI: 10.1038/nmeth.3453

[…] to the read headers with the unix tool awk (awk -f “##” ‘{sub(/..../, “##”$2, $2); getline($3); $4 = substr($3,1,2); $5 = substr($3,3); print $1 $2 $4 “\n”$5}’). for the hek293 mrna dataset (cims miclip), reads from the four replicates were combined at this point. sequence-based removal of pcr duplicates was then performed with the pyfastqduplicateremover.py script. awk was then used […]


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MiClip in publications

 (18)
PMCID: 5882793
PMID: 29643844
DOI: 10.3389/fmicb.2018.00576

[…] a 100–200 nt resolution, employed the pa-m6a-seq strategy, which has an improved resolution (around 30 nt) but requires that the m6a site has a nearby site for 4su incorporation (). the use of the miclip strategy (), which has single-nucleotide resolution, will be instrumental in precisely map the m6a sites present along the hiv-1 grna., similar discrepancies arise from the binding sites […]

PMCID: 5870302
PMID: 29587823
DOI: 10.1186/s13045-018-0590-8

[…] not introduce errors during reverse transcription that would allow direct mapping of its position []. a novel method called m6a individual-nucleotide-resolution crosslinking and immunoprecipitation (miclip) has marked a major step forward in the field, which augments m6a-seq with uv-induced crosslinking of the antibody to the immunoprecipitated rna fragments []. reverse transcription […]

PMCID: 5789076
PMID: 29379020
DOI: 10.1038/s41467-017-02770-z

[…] properties of hnrnp a2/b1. for this analysis, we used a set of 186 nuclear m6a sites comprising m6a sites in xist, neat1, and malat1, which have been mapped at single-nucleotide resolution using miclip (m6a individual-nucleotide-resolution crosslinking and immunoprecipitation). in this analysis, we quantified binding at each of these 168 mapped m6a residues by assigning each m6a residue […]

PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] cells., to identify the mrnas that are methylated in molm13 cells, we mapped m6a at single-nucleotide resolution using m6a individual-nucleotide resolution cross-linking and immunoprecipitation (miclip). in line with our previous analysis, m6a sites were primarily found in both the exons and 3′utrs (52.4% and 32.4% respectively) with the highest enrichment of m6a residues located near […]

PMCID: 5737695
PMID: 28977517
DOI: 10.1093/nar/gkx778

[…] over input (rnaseq) in at least two replicates. this resulted in a total number of 46 186 binding clusters in 9224 exons. this is comparable to the number of peaks obtained in the recent m6a miclip analysis, which revealed 27 771 m6a peaks in 11,880 exons (). we observed high correlation of read counts in fto binding clusters as well as mrna exons and mrna introns (). unfiltered […]


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MiClip institution(s)
Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA

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