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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Queries on Isoseq data in braker #799

Closed karthickbrlab closed 2 months ago

karthickbrlab commented 2 months ago

hi. I processed isoseq data and aligned with genome using minimap. Now how can i proceed to use the bam file in braker.

Im unable to use the singularity for isoseq data. can i use same protocol as RNAseq data using stringtie?

I tried doing this. I found the floowing errror. stringtie is required by GeneMark-ETP but it is not an executable file in your $PATH!

Kindly provide your suggestions

KatharinaHoff commented 2 months ago

I interprete this as you are not using our container but you are dealing with a local custom software installation. I recommend that you have a look at our Dockerfile https://github.com/Gaius-Augustus/BRAKER/blob/master/Dockerfile lines 206-213 (you need to activate those commented lines). That's where you see what GeneMark-ETP we a cloning and what branch we are checking out. A minimal modification is required in ETP to assemble the long read mapping file with StringTie. Either pull that particular ETP branch, or make the local modification, yourself.

ETP comes with a subfolder tools. You may have to add that to your path. stringtie sits in the tools folder.

karthickbrlab commented 2 months ago

Im quite new to linux,

How can i pull that particular branch. or can i just use dockerfile to do so?

Im having some issues with singularity.

thank you

On Wed, Apr 10, 2024 at 1:25 PM Katharina Hoff @.***> wrote:

I interprete this as you are not using our container but you are dealing with a local custom software installation. I recommend that you have a look at our Dockerfile https://github.com/Gaius-Augustus/BRAKER/blob/master/Dockerfile lines 206-213 (you need to activate those commented lines). That's where you see what GeneMark-ETP we a cloning and what branch we are checking out. A minimal modification is required in ETP to assemble the long read mapping file with StringTie. Either full that particular ETP branch, or make the local modification, yourself.

ETP comes with a subfolder tools. You may have to add that to your path. stringtie sits in the tools folder.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/799#issuecomment-2046798079, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQ4H42QDOYZ7DDZAY6DUDDY4TV5LAVCNFSM6AAAAABF734PISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBWG44TQMBXHE . You are receiving this because you authored the thread.Message ID: @.***>

KatharinaHoff commented 2 months ago

You may want to either find someone who helps you install Singularity, or take a bash online course. Then ask ChatGPT (or similar service) to convert the docker directives into bash commands. Sorry, I cannot provide support to learn bash. We provide the container because we don't have the resources to support installation issues.

karthickbrlab commented 2 months ago

Thanks for the info.

On Wed, 10 Apr, 2024, 5:50 pm Katharina Hoff, @.***> wrote:

You may want to either find someone who helps you install Singularity, or take a bash online course. Then ask ChatGPT (or similar service) to convert the docker directives into bash commands. Sorry, I cannot provide support to learn bash. We provide the container because we don't have the resources to support installation issues.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/799#issuecomment-2047397986, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQ4H4YBTOMGG4GQQHXM2P3Y4UVANAVCNFSM6AAAAABF734PISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBXGM4TOOJYGY . You are receiving this because you authored the thread.Message ID: @.***>

karthickbrlab commented 2 months ago

I have installed singularity.

Run failed after this error. Could not locate command line parameters file: /home/ubuntu/.augustus/parameters/aug_cmdln_parameters.json.

how to solve this? can i add the path to config manually?

In case if a braker run failed. Is there any option to continue the run or otherwise i should start it again freshly.

Thank you

KatharinaHoff commented 2 months ago

Please delete the folder /home/ubuntu/.augustus (or place the missing file in the correct location).

kbsivakumar @.***> schrieb am Fr. 12. Apr. 2024 um 13:36:

I have installed singularity.

Run failed after this error. Could not locate command line parameters file: /home/ubuntu/.augustus/parameters/aug_cmdln_parameters.json.

Is there any option to continue the run or otherwise i should start it again freshly.

Thank you

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/799#issuecomment-2051589763, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JHW3JX4WD6LFPNXXW3Y47BK5AVCNFSM6AAAAABF734PISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJRGU4DSNZWGM . You are receiving this because you were assigned.Message ID: @.***>

karthickbrlab commented 2 months ago

Worked well. Thanks for your assistance

karthickbrlab commented 2 months ago

hi.

sorry for frequent queries.

I have done braker predictions with isoseq data and protein data.

I have used protein models from arabidopsis and i got 30000 genes, next i have used entire orthodb- viridiplantae protein data, in that run i got 58000 genes.

So which one could be appropriate and good to go?

thank you

KatharinaHoff commented 2 months ago

Have you combined them with TSEBRA? You definitely want to filter our models from the 58000 set, and TSEBRA can do that for you.

kbsivakumar @.***> schrieb am Mo. 15. Apr. 2024 um 09:02:

hi.

sorry for frequent queries.

I have done braker predictions with isoseq data and protein data.

I have used protein models from arabidopsis and i got 30000 genes, next i have used entire orthodb- viridiplantae protein data, in that run i got 58000 genes.

So which one could be appropriate and good to go?

thank you

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/BRAKER/issues/799#issuecomment-2055723983, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JBNDABZFSVCEHNPJBLY5N3PLAVCNFSM6AAAAABF734PISVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJVG4ZDGOJYGM . You are receiving this because you were assigned.Message ID: @.***>

karthickbrlab commented 2 months ago

Yes singularity run had included TSEBRA for transcript selection and i got it from the log file.

So should i go for predictions made from arabidopsis protein model?