Fwd: methylKit for bioModal duet evoc output

[Alexander Blume]

---------- Forwarded message ---------
Von: Alexander Blume <alex....@gmail.com>
Date: Mi., 19. Juni 2024 um 14:29 Uhr
Subject: Re: methylKit for bioModal duet evoc output
To: <hli...@jh.edu>
Cc: <aak...@gmail.com>

Hi Hua,

You can use the methylRawList() or methylRawListDB() constructor to put the objects in the same list, as described in section "6.0.20 How can I merge multiple separate methylRaw objects into a methylRawList?" of the FAQ section. 

However, these constructors will only accept objects of the same type, so you have to convert them to either normal or *DB objects. Please check here for instructions on how to convert the types.

Best,
Alex

Hua Ling <hli...@jh.edu> schrieb am Di., 18. Juni 2024, 19:28:

Thanks Altuna. I was able to read in raw methylation file for both BioModal/illumina and ONT data. It is the same subject running on two different platforms.

Now I am facing another issue. It looks like in order to do some comparison, they need to be in the same list. I can not create a list directly from raw data because the input format was different. Both data are now in methylRaw and methylRawDB. How to combine them into a methylRawListDB? I looked over the menu and only see “unite” function, but it only works when the two data are both in the same list. I also checked “reorganize”, it only does split/extracting but not “merging” 2 samples.

 

Did I miss the function that can merge two “methylRaw” or “methylRawDB” into a methylRawList?

 

Thanks

 

Hua

 

From: Altuna Akalin <aak...@gmail.com>
Sent: Thursday, June 6, 2024 11:20 AM
To: Hua Ling <hli...@jh.edu>
Cc: alex....@gmail.com
Subject: Re: methylKit for bioModal duet evoc output

 

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Hu Hua,

You should be able to read 5hmC and 5mC from the same file as two separate objects I think. You need to use the generic form of the methRead using the pipeline argument and specifying which columns correspond to which values. 

Please try and see if it works, you need to read documentation and find the blogposts I did years ago for examples.

 

Best,

Altuna

 

On Thu, Jun 6, 2024 at 4:58 PM Hua Ling <hli...@jh.edu> wrote:

Dear Altuna and Alex,

My name is Hua Ling and I am using methylKit to analyze methylation data from BioModal (still sequenced on ilmn sequencer). BioModal now has an assay that allows for differentiate 5mc from 5hmc. So the cytosine report for the duet-evoc chemistry has an additional column. I was able to use function “methRead” to read in the regular cytosine report, but not the duet one (see Fig7 and 8 in the attached document). I am wondering if you have a solution for that or plan to add this capability to the function. Currently, I can get around with this by combining column 4 and 6 into one column and read by “methRead”.

 

Thanks!

 

Hua Ling

 

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