Alternatives to classical HiC data analysis

D 2023

Alternatives to classical HiC data analysis

LEXA, Matej and Hedvig HEGYI

Basic information

Original name

Alternatives to classical HiC data analysis

Authors

LEXA, Matej and Hedvig HEGYI

Edition

Bratislava, Workshop on Bioinformatics and Computational Biology (WBCB 2023), p. 14-14, 1 pp. 2023

Publisher

Knižniˇcné a ediˇcné centrum, Fakulta matematiky, fyziky a informatiky, Univerzita Komenského

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Slovakia

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

Abstracts of WBCB 2023

Organization unit

Faculty of Informatics

ISBN

978-80-8147-132-2

Keywords in English

HiC analysis

Abstract

V originále

HiC is a variant of DNA library preparation and sequencing that can provide information about 3D arrangement patterns in chromatin. A typical HiC experiment involves cross-linking chromatin in vivo, fragmenting it in vitro, ligating the fragments in a proximity-dependent manner. Finally a library for paired-end sequencing is created and sequenced by short read sequencing technology [3]. The typical HiC data analysis today is to preprocess HiC sequencing reads, map them to the closest reference genome, and bin mapped pairs by genomic location to obtain a contact matrix that can be visualized. Reliable tools and pipelines exist to carry out such analyses.

Links

GA21-00580S, research and development project

Name: Jak rostlinné transposony přispívají ke "genomové krajině" a organizaci interfázního jádra (Acronym: transpozony)

Investor: Czech Science Foundation

Citovat

LEXA, Matej and Hedvig HEGYI. Alternatives to classical HiC data analysis. Online. In Bronislava Brejova, Matej Lexa. Workshop on Bioinformatics and Computational Biology (WBCB 2023). Bratislava: Knižniˇcné a ediˇcné centrum, Fakulta matematiky, fyziky a informatiky, Univerzita Komenského, 2023, p. 14-14. ISBN 978-80-8147-132-2.

@inproceedings{2342098,
   author = {Lexa, Matej and Hegyi, Hedvig},
   address = {Bratislava},
   booktitle = {Workshop on Bioinformatics and Computational Biology (WBCB 2023)},
   editor = {Bronislava Brejova, Matej Lexa},
   keywords = {HiC analysis},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Bratislava},
   isbn = {978-80-8147-132-2},
   pages = {14-14},
   publisher = {Knižniˇcné a ediˇcné centrum, Fakulta matematiky, fyziky a informatiky, Univerzita Komenského},
   title = {Alternatives to classical HiC data analysis},
   url = {https://compbio.fmph.uniba.sk/epubs/proceedingsWBCB2023.pdf},
   year = {2023}
}

TY  - JOUR
ID  - 2342098
AU  - Lexa, Matej - Hegyi, Hedvig
PY  - 2023
TI  - Alternatives to classical HiC data analysis
PB  - Knižniˇcné a ediˇcné centrum, Fakulta matematiky, fyziky a informatiky, Univerzita Komenského
CY  - Bratislava
SN  - 9788081471322
KW  - HiC analysis
UR  - https://compbio.fmph.uniba.sk/epubs/proceedingsWBCB2023.pdf
N2  - HiC is a variant of DNA library preparation and sequencing that can provide information about 3D arrangement patterns in chromatin. A typical HiC experiment involves cross-linking chromatin in vivo, fragmenting it in vitro, ligating the fragments in a proximity-dependent manner. Finally a library for paired-end sequencing is created and sequenced by short read sequencing technology [3]. The typical HiC data analysis today is to preprocess HiC sequencing reads, map them to the closest reference genome, and bin mapped pairs by genomic location to obtain a contact matrix that can be visualized. Reliable tools and pipelines exist to carry out such analyses.
ER  -

LEXA, Matej and Hedvig HEGYI. Alternatives to classical HiC data analysis. Online. In Bronislava Brejova, Matej Lexa. \textit{Workshop on Bioinformatics and Computational Biology (WBCB 2023)}. Bratislava: Knižniˇcné a ediˇcné centrum, Fakulta matematiky, fyziky a informatiky, Univerzita Komenského, 2023, p.~14-14. ISBN~978-80-8147-132-2.

Detailed Information on Publication Record