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weir12 / DeepEdit

DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using Nanopore direct RNA sequencing
MIT License
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How to get the target_site.bed file #6

Closed acarmas1 closed 1 year ago

acarmas1 commented 1 year ago

Hello,

I'm interested in using DeepEdit to identify A-to-I sites in my directRNA reads. I'm running your test data set, but I realized that for the sh 1.Reads_extract.sh, a target_site.bed file is needed. I was wondering how can I get this for my own data.

I'm looking forward to hearing from you.

Best, Camila

weir12 commented 1 year ago

Hi,

Thank you for your interest in our project. @LongxianChen will be happy to provide further information and assistance, including thetarget_site.bed files.

Best regards, Liang Ou

acarmas1 commented 1 year ago

Perfect, thank you. I'm looking forward to hearing from Longxian Chen :)

LongxianChen commented 1 year ago

Perfect, thank you. I'm looking forward to hearing from Longxian Chen :)

Hi, Camila

Sorry for the late reply, for we were on vacation for the International Workers' Day.

The target_site.bed file contains positional information of any 'A' site that you want to check for possible editing. Because DeepEdit can only predict sites that are located in trained motifs , it is important to ensure that the sites provided in the target_site.bed file are within the motifs that have been trained in order to obtain reliable prediction results.

I can provide a script to help you obtain all the positions located in motifs that have been trained in your data. Because I am currently on a trip and unable to connect to the server, so it may take two or three days before I can upload it. I will try to upload it as soon as possible if you need it.

Best regards, Longxian Chen

acarmas1 commented 1 year ago

Hi Longxian,

Yes, if you can help me with the script to look up for A in the trained motifs. I'll appreciate it.

I'm highly interested in using this software for predicting A-to-I editing sites.

Thanks, Camila

LongxianChen commented 1 year ago

Hi Longxian,

Yes, if you can help me with the script to look up for A in the trained motifs. I'll appreciate it.

I'm highly interested in using this software for predicting A-to-I editing sites.

Thanks, Camila

Hi, Camila,

I have written a script to get the trained motifs for you (Docs/Get_trained_sites.pl). I tested the script using the (Getting_Started/GCF_000002945.1_ASM294v2_rna.fna)file and it works well. You can use it following this command: perl Get_trained_sites.pl /path/to/your/ref_transcripts.fa Docs/Trained_motifs_v1.0.txt Output.txt

Best, Longxian Chen

acarmas1 commented 1 year ago

Perfect, it worked with my reference transcriptome.

Thank you so much.

weir12 commented 1 year ago

Problem resolved