Closed MiphaZ closed 2 years ago
hi @MiphaZ ,
Can I check with you how do you threshold the m6a sites? Furthermore, can I check how many entries are there in data.readcount file?
Thanks for your reply The data.readcount file includes 150 lines and here is part of it:
transcript_id,transcript_position,n_reads ENST00000210444,347,1 ENST00000210444,441,1 ENST00000210444,476,1 ENST00000210444,695,1 ENST00000210444,787,1 ENST00000210444,794,1 ENST00000210444,815,1 ENST00000210444,843,1
I don't quite understand the threshold you point out (please forgive my poor english) , but I just used the default setting in 'quick start' and the total number including low probability-modified sites is 33.
There should be more than 150 lines if you preprocess the entire dataset. Is this the eventalign result from the full HEK293T datasets? I think my data.readcount for HEK293T dataset contains 80000 ish rows with >= 20 reads
Hi YuanMei, this is a demo data, the original HEK293T dataset is hosted here https://www.ebi.ac.uk/ena/browser/view/PRJEB40872?show=reads
On Mon, Apr 18, 2022 at 5:43 PM YuanMei @.***> wrote:
Is this demo data just contains a part of HEK293T dataset?
— Reply to this email directly, view it on GitHub https://github.com/GoekeLab/m6anet/issues/35#issuecomment-1101266903, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE4RFZDDWPANAX3XMQXQI73VFUVFBANCNFSM5TVHNV7A . You are receiving this because you commented.Message ID: @.***>
Hi @chrishendra93
Is there a way to remove threshold >=20 reads or modify the threshold? Thanks!
Hi, I downloaded HEK293T-WT data which includes a eventalign result from xPore and it's preparation is as same as that in your article. I performed m6anet-dataprep and got this warning:
Then I tried m6anet-run_inference and only found 33 m6a sites. Here is my commands:
Could you give me some suggestions about this issue? Thank you very much!