Use several bam files for gene prediction

[lalalagartija]

Hi, I wonder how to pass several bam files to provide evidence for gene prediction. I would like to avoid to use samtools merge not to create chimeras. I am running trinity first on each sample. I will then merge the outputs of trinity into one file.

• Is there a problem to have redundancy in the trinity evidence ?
• If there are no/fex chimeras in the trinity evidence, will the output of samtools merge still be a problem or can it make the difference beween transcripts given the trinity output ?
• If so, what alternative is there to pass severeal bam files to funannotate predict ? Thanks !

[nextgenusfs]

The bamfile input for funannotate predict is only used to generate intron/exon hints files for augustus. It likely will not matter if merged or not.

[nextgenusfs]

The pipeline is setup in funannotate train to pass multiple pairs of Illumina files which get cleaned up and passed to Trinity. If you let funannotate run Trinity all the input files for predict will be generated for you.... https://funannotate.readthedocs.io/en/latest/tutorials.html#genome-assembly-and-rna-seq

[lalalagartija]

I prefer to control the mapping and the Trinity assembly (genome alignment based) before the prediction. Merging the final bam would be a good option after what you said. Thanks !