BRAKER with long read RNA-Seq: which format?

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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BRAKER with long read RNA-Seq: which format? #769

Closed praimondeau closed 3 months ago

praimondeau commented 4 months ago

Hello, I'd like to use iso-seq data to annotate my genome, however, it's unclear to me which file i should use? My samples were multiplexed in one run, so i have one *subreads.bam+bam.pbi, I have flnc.bam and transcripts.fasta but also hifi.reads.fastq.gz and hifi.reads.fasta.gz for the whole run. Thanks

KatharinaHoff commented 4 months ago

If you want to use the docker isoseq container that I presented at PAG, then you need a bam file. The commands that I used to generate the bam file are in the PAG poster at https://github.com/Gaius-Augustus/BRAKER/blob/master/docs/posters/poster_PAG2024.pdf

praimondeau commented 3 months ago

Hi thanks for the link to the poster. It was helpful. If anyone has the same question about format, i used flnc.bam (FLNC reads for my whole run), converted it into fastq with samtools and mapped with minimap2. The annotation was really good! Thank you for this container, so useful!

praimondeau commented 3 months ago

Hi, should i cite something different from the others BRAKER citatiations to refer to your container in publication?

KatharinaHoff commented 3 months ago

The container was introduced with BRAKER3, so that preprint can be cited. https://www.biorxiv.org/content/10.1101/2023.06.10.544449v4

praimondeau @.***> schrieb am Di. 2. Apr. 2024 um 16:32:

Hi, should i cite something different from the others BRAKER citatiations to refer to your container in publication?

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ryvan1021 commented 1 month ago

Hello, when I try to run braker3 through the container using:

docker exec -it 5d43733fc022 braker.pl --genome=mt8_ul_softmasked.fasta --prot_seq=Viridiplantae.fa --bam=flnc_map_mt8.bam --threads=48 --workingdir=braker3

I get this error:

# Tue May  7 21:06:23 2024: Trying to guess CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH
# Tue May  7 21:06:23 2024: Checking /opt/cdbfasta as potential path for $CDBTOOLS_PATH.
# Tue May  7 21:06:23 2024: Success! Setting $CDBTOOLS_PATH to /opt/cdbfasta!
# Tue May  7 21:06:23 2024: ERROR: in file /opt/BRAKER/scripts/braker.pl at line 3347
BAM file /home/jovyan/flnc_map_mt8.bam does not exist.

Any thoughts on what I should do? I tried substituting absolute paths, but I keep getting the same error. Had to run through docker because installing on the cluster with singularity wasn't working for some reason.

Thanks for the great tool!

ryvan1021 commented 1 month ago

Ah never mind, I think I just didn't mount the image correctly. 'docker run' isn't loading anything so I'll see if it works tomorrow.