Fwd: methstate trouble shutting

[Meng Zhou]

Hi Jianping,

Thank you for using methpipe. I'm forwarding you to our team who can also help you for troubleshooting.

It would help us identify the problem if you can share your command line for running methpie and a few lines of your input data (the .mr file).

Best regards,
Meng

---------- Forwarded message ---------
From: Quan Jianping <Jianping...@outlook.com>
Date: Wed, Dec 2, 2020 at 8:01 AM
Subject: methstate trouble shutting
To: meng...@usc.edu <meng...@usc.edu>

Hi Meng,

 

I hope you are doing well! My name is Jianping Quan, and I’m a doctoral student in Zhenfang Wu’s lab at South China Agricultural University. I’m currently studing a project about finding allele specific expression (ASE) and allele specific DNA methylation (ASM). I’m trying to using your Methpipe to analysis our BS-seq data. An error occurred when I used the “methstate” to convert the .mr format file to the epiread format file. The error was: “could not find chrom: 3”. I think that may because my chrom file was not match with .mr file at naming the chromosome. But when I changed the chromosome name in reference file and .mr file to chr[], the error still occourred and became “could not find chrom: chr3”. Our data-mapping was performed by bismark. It was smothly to convert the bismark.bam file to .mr file by to-mr module. The bisulfite conversion rate estimating and single-site methylation levels computing also run well. After a long time trouble shutting, I still can’t find the point is. Can you give me some suggestion for that reasons? Any help will be appreciated.

 

Thanks,

Jianping

[Meng Zhou]

Looks like this issue has been resolved.

Best regards,
Meng

---------- Forwarded message ---------
From: Quan Jianping <Jianping...@outlook.com>

Date: Wed, Dec 2, 2020 at 9:30 AM
Subject: 回复: methstate trouble shooting
To: Meng Zhou <mzho...@gmail.com>

Hi Meng,

 

Thank you for the response. I may have found the reason after I spliting the reference fasta file by chromosome number. Now, everything seems to be fine. Thanks the excellent softwares from your team and thanks for your patient guidance.

 

Thanks,

Jianping

 

 

发件人: Meng Zhou
发送时间: 2020年12月2日 22:21
收件人: meth...@googlegroups.com; Jianping...@outlook.com
主题: Fwd: methstate trouble shutting