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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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visualization the data #78

Open Fatihlrcfs opened 2 years ago

Fatihlrcfs commented 2 years ago

Hi dear,

firstly thank you for providing Deepsignal. I am wondering how can ı visualize the output of Deepsignal? could you offer any package or guideline in order to visualize the output data? Also, I am currently working on the output of Nanopolish with Methyplotlib and Nanomethvis packages and is there any way to transform the output of Deepsignal to the suitable format of Methplotlib/ Nanomethviz. many thanks.

Kind Regards.

PengNi commented 2 years ago

Hi @Fatihlrcfs , thanks for your interest of out tool.

The methylation frequency file in bed/bedmethyl fomat (generated by scripts/call_modification_frequency.py with --bed option) can be directly visualized in IGV.

However, currently deepsignal doesn't support per-read modification visualization. Maybe there is a way to convert the .call_mods.tsv (per-read outputs) file of deepsignal (with the raw BAM file) to modBAM format, which can be visualized by genome browsers and Methplotlib (Ref: https://mobile.twitter.com/adrienleger2/status/1395400611869429762). But I haven't tried it yet.

Another way, which may be similar to modBAM, is to create a bisBAM file (BAM file for IGV in Bisulfite mode) using the per-read outputs of deepsignal and the raw BAM file, where all unmethylated C/Gs are converted to T/As. Vahid, the author of NanoMethPhase, wrote some code for this (it supports converting nanopolish/tombo/deepsignal per-read outputs to bisBAM file, ref: https://github.com/vahidAK/NanoMethPhase/blob/iss5/nanomethphase/main.py#L631). However, the code/pipeline may need some changes, as it was designed for haplotype-aware methylation.

Best, Peng

Fatihlrcfs commented 2 years ago

Hi @PengNi , thanks for the quick response. I am currently new in this field so the last step might be so complicated for me. but ı can work on others. many thanks.

Kind Regars.

Fatihlrcfs commented 1 year ago

hi @PengNi , sorry again me ı wanna ask a quick question which might not be related your package. the command python /cluster/lrcfs/2397405/bin/deepsignal2downloaded/call_modification_frequency.py --input_path sample_fast5s.CG.call_mods.tsv --result_file sample_fast5s.CG.call_mods.frequency.tsv was working fine before but currently I am getting error below Traceback (most recent call last): File "/cluster/lrcfs/2397405/bin/deepsignal2downloaded/call_modification_frequency.py", line 11, in <module> from txt_formater import ModRecord ModuleNotFoundError: No module named 'txt_formater' this might be the cluster issue because ı am using Linux based university cluster system. I checked python (3.8) and additional subpackage are present and my environment for deepsignal is working and stable. do u have any idea why ı am getting this error. thanks for your time have a great weekend.

PengNi commented 1 year ago

Hi @Fatihlrcfs , to run call_modification_frequency.py, there has to be a python file txt_formater.py in the same directory. You can just download these from the scripts dir in this repo.

Fatihlrcfs commented 1 year ago

Hi @PengNi many thanks for quick response. have a great days:)