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Support for CGmap inputs #5
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Hi @harish0201 sure, I'll get working on that for the next version, I'll update you soon! |
Hi @harish0201 I updated Defiant so it now reads CGmap input. Please let me know if it works for you. |
Alright! Thanks for the update. I'll check it now. |
Hi Dave! I'm working on the inputs, but they seem to crash on the wheat genome, I'll parse them out chromosome wise and get back to you. It seems to give me a CRC error on gzipped files though gunzipping them seems to work. |
Hi Harish, Defiant only reads regular ASCII files. I've considered making it to read gz, but I don't know how yet. Please let me know how everything works out. |
Will do! In the mean time, may be trying to use the system calls (zcat or pigz -c) should be better in order to read compressed files! However, I'm facing no issues running on the unzipped files though, so it's all good :) Edit: Duplicate Comment |
Did everything work out? I'd like to close the issue. |
Yup, it seems to have the trick! Sorry I was travelling a bit, so I wasn't able to do. it. BTW, would you be at the PAG? I would to have a chat with you. |
@harish0201 unfortunately, no, but I would have applied had I known about the conference. |
My email is dec986@gmail.com if you have any questions, or would like to chat. |
Hi Dave!
I have recently come across cgmaptools which is a host of tools that can be used to call methylation and other analysis like allele specific methylation, snv calling etc.
The cgmap output can be derived from either post-processing the aligned bams or is one of the outputs from BS-Seeker.
The format as such looks like this:
Where the headers are:
Chromosome Reference_Nucleotide Position Context_Type Context Methylation_Status Methylated_Cyto_Counts Total_Cyto_Counts
The format as such seems to be similar to Bismark's format 5 as per the Readme.
Would it be possible for you to support it?
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