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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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Using Nanopore data #192

Closed Hannah1746 closed 2 years ago

Hannah1746 commented 2 years ago

So I am trying to use this great pipeline on my Nanopore data. I finally got all the programs to install and work together. I am now having troubles with getting the data in the right format to use methpipe. My problem is with the program abismal:

https://github.com/smithlabcode/abismal/issues/5

I wanted see if there is another way of getting my data into the right format without using abismal since they seem to be very responsive on their github.

Thank you for you time and effort, Hannah

terencewtli commented 2 years ago

Hi,

Is your current data in fastq format?

guilhermesena1 commented 2 years ago

Closing because (1) this was discussed in the abismal repo and (2) inactivity, but feel free to reopen if this issue resurfaces