The base composition of sequencing reads depends on the library type (RNA, genomic, bisulfite, ChIP, etc.) and the species, and can often be characteristic for a particular sequencing application. For a while we’ve been thinking about a quality control tool that checks if a given base composition matches the expected base composition for the application. In other words, does my library look like it is supposed to? Some of the code of my last year’s hackathon project (Charades) could easily be adapted to put a given base composition into the wider context, but what’s missing is a collection of base compositions for a variety of sequencing libraries. The immediate task would be to think about how to best collect library base compositions and match them up with meta data about library type for a variety of published applications. I will most likely be working on a different project this year, but I’d be happy to join in with discussions and provide ideas.

Christel Krueger
Author: Christel Krueger

Christel obtained her PhD in Microbiology from the University of Erlangen (Germany) before she joined Wolf Reik’s lab at the Babraham Institute as a postdoc. Over the next decade she worked on several projects related to epigenetics and mammalian development, including imprinting, spatial organisation of the genome and global transcription. With the emergence of epigenomics, Christel started spending less and less time in the lab and more and more time on the computer. In 2016 she joined the Babraham Bioinformatics Core Facility, and since 2017 she is working as a Bioinformatician for Epigenetics. She is involved in projects from several groups within the Epigenetics ISP.

Categories: Project

Christel Krueger

Christel Krueger

Christel obtained her PhD in Microbiology from the University of Erlangen (Germany) before she joined Wolf Reik’s lab at the Babraham Institute as a postdoc. Over the next decade she worked on several projects related to epigenetics and mammalian development, including imprinting, spatial organisation of the genome and global transcription. With the emergence of epigenomics, Christel started spending less and less time in the lab and more and more time on the computer. In 2016 she joined the Babraham Bioinformatics Core Facility, and since 2017 she is working as a Bioinformatician for Epigenetics. She is involved in projects from several groups within the Epigenetics ISP.

12 Comments

Dina Aly

Dina Aly · September 15, 2020 at 9:18 pm

I want to join this project

    Christel Krueger

    Christel Krueger · September 16, 2020 at 7:47 am

    Great! I suggest we meet up Monday morning to discuss details and I can give you more background information!

PATRICIA NABISUBI

PATRICIA NABISUBI · September 16, 2020 at 8:51 am

Commentant so eager to learn everything about databases

    Christel Krueger

    Christel Krueger · September 16, 2020 at 11:30 am

    Dear Patricia, you’re of course very welcome to join this project, but just as a heads-up, the database in question will only be of the simplest kind: pretty much a spreadsheet. The more challenging part will be to define the library types to be included, search publications for them and extract sequencing reads for publicly available datasets.

Edward Tettevi

Edward Tettevi · September 17, 2020 at 6:28 pm

I am very happy to join this project

    Christel Krueger

    Christel Krueger · September 17, 2020 at 9:14 pm

    Excellent – we can meet up Monday morning and discuss some more details!

Boï KONE

Boï KONE · September 18, 2020 at 3:46 pm

Very impressive project and I will be pleased to join it.

Stephen Kanyerezi

Stephen Kanyerezi · September 21, 2020 at 6:46 am

I would love to join

Kanakalakshmi Annamalai

Kanakalakshmi Annamalai · September 22, 2020 at 4:31 pm

Hi…This is Kanakalakshmi Annamalai from India…I would like to join in this project… I hold my degree in Microbiology and I don’t have any experience in programming…

    Christel Krueger

    Christel Krueger · September 23, 2020 at 6:04 am

    Hi Kanakalakshmi! If you would like to join this project for this last day of the hackathon, please join the Teams channel ‘Base Composition – Task 2 Finding Datasets’. There is quite a bit of information on the task in there already and we can chat about specifics.
    Best, Christel

Faridul · September 22, 2020 at 9:07 pm

Hello Dr. Krueger,
I am doing PhD in Plant breeding. I have lots of interest on Epigenetics and currently searching Post doc on epigenetics. With this aim, I am being built up my bioinformatics skills. I am intermediate in scripting in R, Bash and learnt different bioinformatics analysis tools. I was informed about this project lately. I just wonder if there is anyway to work with you regarding on epigenetics to build up the skill?Thanks

    Christel Krueger

    Christel Krueger · September 23, 2020 at 6:03 am

    Hi Faridul! If you would like to join this project for this last day of the hackathon, please join the Teams channel ‘Base Composition – Task 2 Finding Datasets’. There is quite a bit of information on the task in there already and we can chat about specifics.
    Best, Christel

Leave a Reply

Your email address will not be published. Required fields are marked *