icSHAPE-pipe
A pipeline to calculate SHAPE/DMS reactity score
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Latest Release
icSHAPE-pipe 2.0.1
10/11/19
P. Li, R. Shi, Q. Cliff Zhang,
icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation
, Methods (2019)
Secondary structures
Human rRNA
5S/18S/28S/Mito16S
Mouse rRNA
5S/18S/Mito16S
Yeast rRNA
5S/16S/23S/Mito16S
Version 2.0.0 - May 11, 2019
Added the support for Python 3
Added the feature to calculate specific bases (for example: A/C for DMS-Seq)
Added the feature to calculate each type of bases seperately
Added the feature to calculate the reactivity of short transcript without sliding window
Added the feature to show reactivity score distribution
Removed the feature to calculate pearson correlation of replication of reactivity scores
Version 1.0.0 - March 6, 2019
Support for Python 2.7
Support to calculate the reactivity score for each base with the sliding window
Preparation modules --
starbuild
,
parseGTF
Fastq-preprocessing modules --
readcollapse
,
trim
,
cleanFq
Mapping & calculation modules --
mapGenome
,
calcFPKM
,
sam2tab
,
trainParameter
,
calcSHAPE
Coordination system conversion modules --
genSHAPEToTransSHAPE
,
genRTBDToTransRTBD
,
genSHAPEToBedGraph
quality modules --
readDistributionStatistic
,
samStatistics
,
transSHAPEStatistics
,
countRT
,
plotGenomeRTRepCor
,
combine_gTab_SHAPE
,
plotGenomeSHAPERepCor
,
evaluateSHAPE
