Column header _position_ in site_level_prediction

[gsukrit]

Hi team,

I would like to have clarity on the column header position in the output file of site_level_prediction (CHEUI solo outputs). Does it indicate the position of modified base from the start of that particular transcript ID or the coordinate on the genome where that modified base is predicted. If it is the position of the base from the start of that particular transcript, does it start from the mRNA coordinates (starting from the 5' UTR region) on the genome ?

Any idea on this concern further will be highly appreciated.

Thanks,

Sukriti

[EduEyras]

Hi,

Thanks for the email.

The position is the coordinate (half-open) of the 9-mer in the transcript where the prediction is made.

That is, if the number is NNNNANNNN and the location is

5' XXXNNNNANNNNXXX... 3'

The coordinate should be 2, i.e.:

0123456... 5' XXXNNNNANNNNXXX... 3'

I cc Akanksha and Favour who will be able to confirm

Thanks

Eduardo

On Tue, 1 Aug 2023 at 00:39, gsukrit @.***> wrote:

Hi team,

I would like to have clarity on the column header position in the output file of site_level_prediction (CHEUI solo outputs). Does it indicate the position of modified base from the start of that particular transcript ID or the coordinate on the genome where that modified base is predicted. If it is the position of the base from the start of that particular transcript, does it start from the mRNA coordinates (starting from the 5' UTR region) on the genome ?

Any idea on this concern further will be highly appreciated.

Thanks,

Sukriti

— Reply to this email directly, view it on GitHub https://github.com/comprna/CHEUI/issues/24, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBZS4VL3WAAFGAIPKM3XS67S5ANCNFSM6AAAAAA26LTAH4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[gsukrit]

Thank you for your response. Can you please suggest a possible way to map this position to the exact coordinate on the genome from the gff file, i.e. to 5'UTR/CDS/3'UTR ? Or to map it to the exact nucleotide base of that particular transcript ?

Thanks,

Sukriti

[Akanksha2511]

Hi Sukriti,

The position is the position of the first nucleotide in the site column. So for example below

contig              position    site    coverage        stoichiometry   probability
ENST00000000233.10 1003     CTTGAGTAA   648              0.10132158     0.11857438

1003 is the position of C for the site CTTGAGTAA in the transcript ENST00000000233.10. To get the position of the center nucleotide which in this case is A you add 5. So it will be position +5 for the center nucleotide for which the prediction is made. I hope it helps.

Thanks, Akanksha

[gsukrit]

Thank you for the information. That really gave some clarity. Can you suggest a possible approach / method to map these predicted positions to the exact gene coordinate and classify them as UTR / CDS.

Thanks for the assistance.

Regards,

Sukriti

On Wed, Aug 2, 2023, 4:52 AM Akanksha2511 @.***> wrote:

Hi Sukriti,

The position is the position of the first nucleotide in the site column. So for example below

contig position site coverage stoichiometry probability ENST00000000233.10 1003 CTTGAGTAA 648 0.10132158 0.11857438

1003 is the position of C for the site CTTGAGTAA in the transcript ENST00000000233.10. To get the position of the center nucleotide which in this case is A you add 5. So it will be position +5 for the center nucleotide for which the prediction is made. I hope it helps.

Thanks, Akanksha

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[EduEyras]

Hi, yes,

Please have a look at our tool https://github.com/comprna/R2Dtool Here is the preprint https://www.biorxiv.org/content/10.1101/2022.09.23.509222v1

I cc AJ who wrote the software Please let us know if you have any problem with it best

Eduardo

On Wed, 2 Aug 2023 at 14:00, gsukrit @.***> wrote:

Thank you for the information. That really gave some clarity. Can you suggest a possible approach / method to map these predicted positions to the exact gene coordinate and classify them as UTR / CDS.

Thanks for the assistance.

Regards,

Sukriti

On Wed, Aug 2, 2023, 4:52 AM Akanksha2511 @.***> wrote:

Hi Sukriti,

The position is the position of the first nucleotide in the site column. So for example below

contig position site coverage stoichiometry probability ENST00000000233.10 1003 CTTGAGTAA 648 0.10132158 0.11857438

1003 is the position of C for the site CTTGAGTAA in the transcript ENST00000000233.10. To get the position of the center nucleotide which in this case is A you add 5. So it will be position +5 for the center nucleotide for which the prediction is made. I hope it helps.

Thanks, Akanksha

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[gsukrit]

Hi team,

So I tried running the suggested R2Dtool. The CHEUI output file (site_level_5mC_prediction) looked like this:

The command bash cheui_to_bed.sh [cheui model II output file] [cheui_to_bed output file] created a file that looked like this:

For some reason it hasn;t copied the complete gene accession IDs. Probably the reason why Rscript ./scripts/R2_annotate.R ./test/out_CHEUI_modelII.bed ./test/GRCm39_subset.gtf ./test/out_CHEUI_modelII_annotated.bed gave the following error:

Please let me know what went wrong and how to proceed further.

Thank you for your response and efforts,

Sukriti

[pre-mRNA]

Hi Sukriti, apologies for the delay.

You can try the latest version of R2Dtool, which should resolve this error:

https://github.com/comprna/R2Dtool