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weir12 / DENA

Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.
MIT License
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ouput explaination of LSTM_predict.py #12

Closed defendant602 closed 2 years ago

defendant602 commented 2 years ago

HI, Thanks for the great work you've done! I am using this software and get two tsv files after runing LSTM_predict.py.

As shown in the mainpage, the tsv files have transcript id and m6A sites, but what do the rest columns mean ? would appreciate some more detained explainations about the output files.

  Thanks.
q1134269149 commented 2 years ago

Hi,

Thank you very much for your advice. For example: AT1G01010.1 30 AAACA 0 3 0.0 AT1G01010.1 212 AAACA 0 5 0.0 AT1G01010.1 341 AAACA 1 5 0.2

First column: Transcript ID; Second column: Transcriptional coordinate of the central "A" base in RRACH motif; Third column: Motif of candidate sites； Fourth column: The number of modified reads; Fifth column: The number of total reads; Sixth column: The m6A ratio predicted at this site.

If our tools are helpful to you, please help us light up the Star in Github. Thank you！

qinhang

weir12 commented 2 years ago

Hi, Thank you for your interest in our project.

image

This image may help explain the last three columns of the output file. Please feel free to contact us whenever you have a question. Liang Ou

zzf77 commented 1 year ago

Hi,

Thank you very much for your advice. For example: AT1G01010.1 30 AAACA 0 3 0.0 AT1G01010.1 212 AAACA 0 5 0.0 AT1G01010.1 341 AAACA 1 5 0.2

First column: Transcript ID; Second column: Transcriptional coordinate of the central "A" base in RRACH motif; Third column: Motif of candidate sites； Fourth column: The number of modified reads; Fifth column: The number of total reads; Sixth column: The m6A ratio predicted at this site.

If our tools are helpful to you, please help us light up the Star in Github. Thank you！

qinhang

Hi, Thank you for your tools, but I have two questions about the result of this step. Is the tsv file format the same as the bed format? Does the second column of the tsv files start at 0 or 1? Due to I need to use the bedtools next, which requires the files in the format of bed. Thanks!