bismark + mcall

[aaron.l...@gmail.com]

So I managed to get moabs to compile (had to use R 2.15.3, and manually install Rcpp from http://dirk.eddelbuettel.com/code/rcpp/Rcpp_0.9.15.tar.gz, then install RInside from CRAN)

The documentation says it is possible to use mcall on bismark aligned files, however I can't see an option for mcall to interpret the XG/XR tags used by bismark - does this happen automatically?

[Deqiang Sun]

I am sorry I was on a travel and then engaged into a few deadlines and did not have time to check this email address. Thanks for finding out a solution. Yes I do have adapted my program to accept bismark files a long time ago, probably 2 years ago. Let me check if the proper version is included and get back to you. 

On Sun, Dec 8, 2013 at 8:07 PM, <aaron.l...@gmail.com> wrote:

So I managed to get moabs to compile (had to use R 2.15.3, and manually install Rcpp from http://dirk.eddelbuettel.com/code/rcpp/Rcpp_0.9.15.tar.gz, then install RInside from CRAN)

The documentation says it is possible to use mcall on bismark aligned files, however I can't see an option for mcall to interpret the XG/XR tags used by bismark - does this happen automatically?

--
You received this message because you are subscribed to the Google Groups "MOABS Discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to moabs_msuite...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.

[smitht...@gmail.com]

Hi Deqiang,

Could you let me know how to run mcall on a Bismark-generated BAM. I'm currently getting the following error message:
"XR:Z or ZR:Z:, or ZS:Z: field not found, please enable -R option in bsmap"

Command: mcall -m Liver-Saline-1.fastq.gz_bismark_bt2.sorted.bam --outputDir testdir -g rn5 -r /ifs/mirror/genomes/plain/rn5.fasta --skipRandomChrom 1 2>log

Kind regards,

Tom

[bped...@gmail.com]

I get this same error with bismark files and the test files provided. The program segfaults after a bit.

[jeni j]

Hello,

I have bismark mapped and methylation extracted data. I really like this tool for DMR identification. But the *.sam files are not working fine in mcall. I also removed the XR: col still I am getting the error as Segmentation Fault (core dumped).

I would be more interested to convert methylation cytosince extraction output to input of mcomp, so that I can directly go for DMR analysis.

So, my question is How to use moabs (or mcomp or mcall) to identify DMR from any output of bismark pipeline?

Thanks in advance.

[tasmany]

Hi,

I also provided bam file which is generated by Bismark to mcall, and got the same error Segmentation Fault (core dumped). I run this tool on ubuntu 14.04.

Thanks in advance

[yuful...@gmail.com]

在 2014年10月13日星期一 UTC+8下午8:17:31，jeni j写道：

Hi, jeni
Have you found any solution? I have the same problem