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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 RNA-seq and Isoseq data in braker #804

Open lidachuis opened 5 months ago

lidachuis commented 5 months ago

hi， I have a sample, and this sample has rnaseq data and isoseq data

braker.pl --genome=genome.fasta --prot_seq pro.fasta --bam=rnaseq.bam --bam=iso_seq.bam --threads 32

Is this command running correctly?

I don't know much about how to use isoseq in braker3.

KatharinaHoff commented 5 months ago

No. The two bam files can currently not be processed by the same container/in one braker.pl run. Unless you modified GeneMark-ETP locally for this. Then, the command would still be wrong, —bam can only be provided once.

lidachuis @.***> schrieb am Mo. 15. Apr. 2024 um 03:55:

hi， I have a sample, and this sample has rnaseq data and isoseq data

braker.pl --genome=genome.fasta --prot_seq pro.fasta --bam=rnaseq.bam --bam=iso_seq.bam --threads 32

Is this command running correctly?

I don't know much about how to use isoseq in braker3.

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lidachuis commented 5 months ago

Hi I found that there is a branch long_reads in braker3. Can this branch solve the situation of iso-seq and rna-seq data? [https://github.com/Gaius-Augustus/BRAKER/blob/long_reads/docs/long_reads/long_read_protocol.md]

At the same time, I also tried docker braker3:isoseq, but there was an error in its operation. The error was that bamtools was not found.

KatharinaHoff commented 5 months ago

The missing bamtools issue is one that I really fail to understand. Someone else independently reported that a while ago, and I cannot reproduce it. Here is how it looks when I run the container in singularity:

singularity exec braker_lr.sif which braker.pl
/opt/BRAKER/scripts/braker.pl
singularity exec braker_lr.sif which bamtools
/usr/bin/bamtools
singularity exec braker_lr.sif echo $PATH
/opt/singularity-3.11.3/lib/:/opt/singularity-3.11.3/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

Is the PATH different on your system? bamtools sits in /usr/bin, and that should be in the PATH.

BRAKER has the option to receive the location of bamtools as command-line argument. But I think that did not help the other user who reported a similar issue.

The long read protocol is outdated to some extent. You may find the TSEBRA combiner advice at the end helpful. The protocol itself still builds on cupcake, most people don't use cupcake, anymore. It also does not filter the isoseq transcripts very well, that should work a lot better with GeneMark-ETP.

lidachuis commented 5 months ago

Hi，KatharinaHoff I failed to use docker's isoseq before, and now I have successfully executed isoseq using singularity. Now I have a new question, that is, I generated a braker.gtf through isoseq of the container, and also generated a braker.gtf using the data of rnaseq. How can I integrate them?

KatharinaHoff commented 5 months ago

You can run TSEBRA to merge them.

lidachuis @.***> schrieb am Do. 18. Apr. 2024 um 04:55:

Hi，KatharinaHoff I failed to use docker's isoseq before, and now I have successfully executed isoseq using singularity. Now I have a new question, that is, I generated a braker.gtf through isoseq of the container, and also generated a braker.gtf using the data of rnaseq. How can I integrate them?

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lidachuis commented 5 months ago

Thank you. Then should I use TSEBRA in the long_reads branch or tesbra in the master branch?

KatharinaHoff commented 5 months ago

You probably want to test several runs, either way. Luckily TSEBRA is much faster than BRAKER.

lidachuis @.***> schrieb am Do. 18. Apr. 2024 um 05:35:

Thank you. Then should I use TSEBRA in the long_reads branch or tesbra in the master branch?

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