CHEUI model 2: prediction of stoichiometry and modification probability at transcriptomic sites : Executed with Error

[gsukrit]

Hi team,

I was trying to run the command: python3 ../scripts/CHEUI_predict_model2.py -i read_level_m6A_predictions_sorted.txt -m ../CHEUI_trained_models/CHEUI_m6A_model2.h5 -o site_level_m6A_predictions.txt

The command got executed, and the site-level file was made, but it also gave an error. I've attached a screenshot for the same.

Any assistance with this will be highly appreciated.

Thanks,

[Akanksha2511]

Hi,

I think it is related to the version of TensorFlow installed.

Can you please try replacing the below line in the CHEUI_predict_model2.py code

lr_probs = model.predict(prob_vectors) to: lr_probs = model.predict(prob_vectors.reshape(prob_vectors.shape[0], 99, 1))

It should be line number 199 and 220 in CHEUI_predict_model2.py.

Please let us know if it helps.

Thanks, Akanksha

[EduEyras]

Thanks for your email

This might be a problem with TensorFlow I cc Akanksha who may be able to help with this

Thanks

Eduardo

On Fri, 21 Jul 2023 at 16:22, gsukrit @.***> wrote:

Hi team,

I was trying to run the command: python3 ../scripts/CHEUI_predict_model2.py -i read_level_m6A_predictions_sorted.txt -m ../CHEUI_trained_models/CHEUI_m6A_model2.h5 -o site_level_m6A_predictions.txt

The command got executed, and the site-level file was made, but it also gave an error. I've attached a screenshot for the same.

[image: Screenshot (141)] https://user-images.githubusercontent.com/81628564/255089644-d4d5e979-d5c6-4958-b4ce-e8b4dea624de.png [image: Screenshot (142)] https://user-images.githubusercontent.com/81628564/255089649-23886851-c01a-41a5-a7b4-d3b8bb4f2062.png

Any assistance with this will be highly appreciated.

Thanks,

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[gsukrit]

The command got executed without any errors this time.

Thank you so much for the help.

[gsukrit]

Hi,

I was able to execute the command without any errors this time. Thank you so much for the help.

I have another query. The CHEUI documentation says these estimations are based on alignments in the positive strand and include the samtools view -F 2324 -b flag during alignment. However, I have not included that flag in my alignment file. The command used by me was:

~/minimap2/minimap2 -a -x map-ont | ~/samtools-1.3.1/samtools sort -T tmp -o output.sorted.bam

~/samtools-1.3.1/samtools index output.sorted.bam

Should that be a problem with the accuracy of the results? Please let me know.

Thanks again,

On Fri, Jul 21, 2023 at 12:13 PM Akanksha2511 @.***> wrote:

Hi,

I think it is related to the version of TensorFlow installed.

Can you please try replacing the below line in the CHEUI_predict_model2.py code

lr_probs = model.predict(prob_vectors) to: lr_probs = model.predict(prob_vectors.reshape(prob_vectors.shape[0], 99, 1))

Please let us know if it helps.

Thanks, Akanksha

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[EduEyras]

Hi,

Thanks for letting us know.

It is rare that RNA reads map in the reverse strand but it can happen. You could check how often that occurs in your BAM output. If there are none or very few, it should then be fine. But we usually don't know until we check.

An alternative is to rerun the analysis ...

I hope this helps

best

Eduardo

On Fri, 21 Jul 2023 at 22:32, gsukrit @.***> wrote:

Hi,

I was able to execute the command without any errors this time. Thank you so much for the help.

I have another query. The CHEUI documentation says these estimations are based on alignments in the positive strand and include the samtools view -F 2324 -b flag during alignment. However, I have not included that flag in my alignment file. The command used by me was:

~/minimap2/minimap2 -a -x map-ont | ~/samtools-1.3.1/samtools sort -T tmp -o output.sorted.bam

~/samtools-1.3.1/samtools index output.sorted.bam

Should that be a problem with the accuracy of the results? Please let me know.

Thanks again, … https://github.com/comprna/CHEUI/issues/23#

— Reply to this email directly, view it on GitHub https://github.com/comprna/CHEUI/issues/23#issuecomment-1645508905, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKB6YDTNAB7LLMFK5TXTXRJZGDANCNFSM6AAAAAA2SMQAJQ . You are receiving this because you commented.Message ID: @.***>