Repliscan

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.

Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.

Repliscan is described in the following publication:

Zynda, G., Song, J., Concia, L. et al. Repliscan: a tool for classifying replication timing regions. BMC Bioinformatics 18, 362 (2017). https://doi.org/10.1186/s12859-017-1774-x

Published07 August 2017

DOI https://doi.org/10.1186/s12859-017-1774-x

Mandatory arguments

Parameters

• scope: Replication scope [chromosome, genome]

• percentile cutoff: Remove the upper and lower % of the data when using percentile as remove

• log: Apply log transform to sequenceability ratio

• aggregate: Replicate agregation method [sum, median, mean, min, max]

• value: Explicit replication threshold value when using threshold as value

• classifier: Segmentation classification method [binary, proportion]

• Plot: Plot Statistics of input coverage histograms and for cubic and derivative interpolation for each chromosome

• threshold: Replication threshold method [value, auto, percent]

• percent: Remove the lowest % of signal as noise when using threshold as percent

• remove: Outlying data to remove [none, sqrtGamma, lognGamma, norm, whiskers, percentile]

• Haar smoothing level: Haar smoothing level [1,2,3,4,5]

• Analysis bin size in base pairs: 1000

Test Run

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data >repliscan

(/iplant/home/shared/iplantcollaborative/example_data/repliscan)

Mandatory arguments: 

• Use  input_ds.txt and folder for files listed on list of bams
  
  These alignment files: bams are from maize samples, have been downsampled and do not include biological replicate information hence, this does not represent the full dataset on our initial analyses and provided for testing purposes.
  
  

• Parameters used for test data:

• -Reference genome in Fasta format

Parameters:

Leave all the values as they are for default settings.

Output

In the case of test run, the output folder contains bedgraph files and gff3 files