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Re: Outreachy project: complete workflows of tools


My name is Shruti. I have been contributing to Debian Med by writing autopkgtests for which I will be applying through GSoC this year. 
However, I came across this project which really interests me. I was initially planning on applying for this through Outreachy but unfortunately my application was not approved. 

I have a background in wet lab and I have worked extensively with RNA-Seq and microarray workflows for analysis of clinical data (particularly lymphoma). Last summer I worked on harmonising cell line datasets (RNA-Seq and microarray) to identify biomarkers and molecular signatures driving immune resistance for chemotherapy in DLBCL patients. I would be happy to learn other workflows such as microbiomes, CHiP-Seq etc if needed. 

I would love to be able to work on this project since it aligns with my skills sets, however I noticed that this project is not available through GSoC. Would it be possible to offer this project through GSoC as well so that I can submit a proposal for this? 

Thanking you, 

On Mon, Mar 8, 2021 at 5:19 PM Tony Travis <tony.travis@minke-informatics.co.uk> wrote:
On 07/03/2021 23:47, Tassia Camoes Araujo wrote:
> Hi all,
> On 2021-03-05 11:09, Tassia Camoes Araujo wrote:
>> [...]
>> Since deadline is approaching quickly, I suggest we move this off-list
>> and start writing in a wiki or pad.
> Here is my first draft, pasted below for your reference, but you can
> edit the text directly in this pad:
> https://storm.debian.net/shared/OCYsOOEqJ5-CcfjVxIiye-ex-4LheegyP1pkIFghMKa
> Help needed to write the Intern tasks section. Also, please check if you
> have better scientific articles to recommend and list a few tools to be
> used in the starter tasks.
> Please help shaping this proposal so it ***really*** makes sense and
> attract interns ;-)

Hi, Tassia.

I recommend using "flexbar", which I use, instead of "Trimmomatic":

> https://github.com/seqan/flexbar

Also, depending on the sequencing technology used, consider assembling
short-paired-end reads with e.g. Pear:

> https://github.com/tseemann/PEAR



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