PMID- 32850708
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20200928
IS  - 2296-4185 (Print)
IS  - 2296-4185 (Electronic)
IS  - 2296-4185 (Linking)
VI  - 8
DP  - 2020
TI  - Assessing the Impact of Data Preprocessing on Analyzing Next Generation 
      Sequencing Data.
PG  - 817
LID - 10.3389/fbioe.2020.00817 [doi]
LID - 817
AB  - Data quality control and preprocessing are often the first step in processing 
      next-generation sequencing (NGS) data of tumors. Not only can it help us evaluate 
      the quality of sequencing data, but it can also help us obtain high-quality data 
      for downstream data analysis. However, by comparing data analysis results of 
      preprocessing with Cutadapt, FastP, Trimmomatic, and raw sequencing data, we 
      found that the frequency of mutation detection had some fluctuations and 
      differences, and human leukocyte antigen (HLA) typing directly resulted in 
      erroneous results. We think that our research had demonstrated the impact of data 
      preprocessing steps on downstream data analysis results. We hope that it can 
      promote the development or optimization of better data preprocessing methods, so 
      that downstream information analysis can be more accurate.
CI  - Copyright (c) 2020 He, Zhu, Yang, Lu, Wang, Song, Sun, Zhang, Li, Yang, Tian, Bing 
      and Lang.
FAU - He, Binsheng
AU  - He B
AD  - Academician Workstation, Changsha Medical University, Changsha, China.
FAU - Zhu, Rongrong
AU  - Zhu R
AD  - Vascular Surgery Department, Tsinghua University Affiliated Beijing Tsinghua 
      Changgung Hospital, Beijing, China.
FAU - Yang, Huandong
AU  - Yang H
AD  - Department of Gastrointestinal Surgery, Yidu Central Hospital of Weifang, 
      Weifang, China.
FAU - Lu, Qingqing
AU  - Lu Q
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Wang, Weiwei
AU  - Wang W
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Song, Lei
AU  - Song L
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Sun, Xue
AU  - Sun X
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Zhang, Guandong
AU  - Zhang G
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Li, Shijun
AU  - Li S
AD  - Department of Pathology, Chifeng Municipal Hospital, Chifeng, China.
FAU - Yang, Jialiang
AU  - Yang J
AD  - Academician Workstation, Changsha Medical University, Changsha, China.
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Tian, Geng
AU  - Tian G
AD  - Geneis Beijing Co., Ltd., Beijing, China.
FAU - Bing, Pingping
AU  - Bing P
AD  - Academician Workstation, Changsha Medical University, Changsha, China.
FAU - Lang, Jidong
AU  - Lang J
AD  - Geneis Beijing Co., Ltd., Beijing, China.
LA  - eng
PT  - Journal Article
DEP - 20200730
PL  - Switzerland
TA  - Front Bioeng Biotechnol
JT  - Frontiers in bioengineering and biotechnology
JID - 101632513
PMC - PMC7409520
OTO - NOTNLM
OT  - HLA typing
OT  - cancer
OT  - data preprocessing
OT  - mutation
OT  - the next generation sequencing
EDAT- 2020/08/28 06:00
MHDA- 2020/08/28 06:01
PMCR- 2020/01/01
CRDT- 2020/08/28 06:00
PHST- 2020/04/05 00:00 [received]
PHST- 2020/06/26 00:00 [accepted]
PHST- 2020/08/28 06:00 [entrez]
PHST- 2020/08/28 06:00 [pubmed]
PHST- 2020/08/28 06:01 [medline]
PHST- 2020/01/01 00:00 [pmc-release]
AID - 10.3389/fbioe.2020.00817 [doi]
PST - epublish
SO  - Front Bioeng Biotechnol. 2020 Jul 30;8:817. doi: 10.3389/fbioe.2020.00817. 
      eCollection 2020.