Journal article Open Access

Script used for the study 'Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis'.

Jo, Se-Young; Kim, Eunyoung; Kim, Sangwoo

Introduction

Scripts used for the study 'Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analyis'. ConcatRef, Disambiguate and XenofilteR are the best suggested filtering method for general purpose. Alternatively, Xenome, XenofilteR and ConcatRef are also recommended for SNV analysis. After applying filtering method, further filtering can be achieved by blacklisting using HAMA list. Estimation of contamination ratio can be used as an indicator of whether strict or lenient blacklisting should be applied.

Description

  • Filtering Methods

    • BBsplit
    • Bamcmp
    • ConcatRef
    • Disambiguate
    • TwinRef-L
    • TwinRef-S
    • XenofilteR
    • Xenome
       
  • MouseContamEstimator

    • Simple Python script for calculating estimated contamination level.
      MouseContamEstimator requires HAMAlist.

Files (10.4 kB)
Name Size
MouseContamEstimator.py
md5:1bdf21b54dc1fc8b9a9c23cceaeaaed0
1.7 kB Download
pipe_Bamcmp.sh
md5:9da47db7cbaee357296b08f9c668fa1d
2.1 kB Download
pipe_BBsplit.sh
md5:da9e5bece2c89627b487d6137b31d299
307 Bytes Download
pipe_BBsplit_making_merged_ref.sh
md5:96134a707567edcdda0a79bd6bd8d9db
324 Bytes Download
pipe_ConcatRef.sh
md5:483eb3e100ac16225fb539f511af4b2e
1.1 kB Download
pipe_Disambiguate.sh
md5:82f1172a0993bacdf891cf67626c655e
1.6 kB Download
pipe_DualRef-L.sh
md5:8f5d738f9cccfdb83351ad6016220b1c
969 Bytes Download
pipe_DualRef-S.sh
md5:749ac496bfd3621f85eb66c0ee54f027
980 Bytes Download
pipe_XenofilteR.R
md5:ad40e460b9019840dcef333732fa85bf
464 Bytes Download
pipe_Xenome_classify.sh
md5:76340b499e07de637bc4d5699f1b365e
586 Bytes Download
pipe_Xenome_index.sh
md5:212212c59545318e6cd7c027caa4cdbc
253 Bytes Download
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