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.
- Simple Python script for calculating estimated contamination level.
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 |
281
140
views
downloads
| All versions | This version | |
|---|---|---|
| Views | 281 | 281 |
| Downloads | 140 | 140 |
| Data volume | 138.7 kB | 138.7 kB |
| Unique views | 263 | 263 |
| Unique downloads | 90 | 90 |
Indexed in
- Publication date:
- September 30, 2019
- DOI:
-
- Keyword(s):
- PDM, PDX, organoid, mouse, filtering, NGS
- License (for files):
- Creative Commons Attribution 4.0 International