MiClip pipeline

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 pipeline

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 script30. awk was then used […]

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

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