MUSiCC User Manual MUSiCC>Web
Contents
1. MUSiCC User Manual MUSICC is a toolkit for correcting biases in gene abundance measurements derived from shotgun metagenomic sequencing and is available as an online tool and as a Python module MUSiCC is developed by the Borenstein group at the University of Washington and is available online at http elbo gs washington edu software_musicc html MUSiCC gt Web MUSiCC gt Web allows researchers to normalize and correct their metagenomic gene abundance measurements online and requires only a web browser The MUSiCC gt Web application is built on top of the MUSiCC gt Python module Overview of use To normalize and correct the abundance measurements of genes using MUSiCC gt Web the user simply uploads their gene abundance file to the MUSICC server by filling out the form shown in Figure 1 a After checking the integrity of the file MUSiCC gt Web normalizes and corrects the measured abundance A link to the file containing the corrected abundances is displayed along with statistics of the data and correction procedures as shown in Figure 1 b A MUSICC Metagenomic Universal Single Copy Correction Gene Abundance Choose File No file chosen KEGG Orthology Groups KO 4 Correct inter sample variation Correct intra sample variation Use our generic model 2 Correct Abundances B Thank you for using MUSICC You can download the corrected abundance file here Here are some2. rect inter sample variation Selecting this will perform the normalization step of MUSICC correcting inter sample variation Correct intra sample variation Selecting this will perform the intra sample correction with the generic model learned from the Human microbiome project HMP stool samples Citing information If you use the MUSICC software please cite the following paper MUSICC A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome Ohad Manor and Elhanan Borenstein Submitted
3. statistics from your data Number of samples 134 Number of genes 13328 MUSIiCC Normalization We corrected inter sample variation using the set of universal single copy genens Number of Universal single copy genes found 76 76 MUSIiCC Correction We corrected intra sample variation Model used Generic model Number of genes corrected by model 3912 Fig 1 The MUSiCC gt Web interface A The user is first presented with a form to upload the abundance file and select the analysis options B The gene abundance file is corrected and available for download along with statistics collected during the correction Setting up the analysis Selecting the abundance file to correct Choose File Browse Select the abundance file on your local drive In the drop down box below choose the appropriate file type MUSiCC gt Web supports abundance files formatted as plain text with various delimiters Gene abundance files have one line per gene with the gene ID appearing as a row header followed by all the abundance measurements corresponding to different samples separated by a space comma or tab Each line must use the same separating character The first line of the file must contain column headers with names for each sample with the first cell in the line containing any string e g KO Analysis Options Once you have specified the abundance file the next step is to choose what types of corrections should be applied to the data Cor
Download Pdf Manuals
Related Search