Hi everyone 👋

I’m Eva, a master’s student who’s still new to bioinformatics.

I’m using the nf-core/RNAsplice pipeline (Nextflow) to analyse my RNA-seq data, but I’m running into an error I can’t resolve. I’m running the pipeline with BAM files generated from a previous STAR alignment.

In the pipeline, I selected the input type as transcriptome BAM files and used the same reference genome that I aligned to previously. However, I keep getting the error in the picture during the

SALMON_QUANT_STAR

process:

It says something like “Transcript chr14 appeared in the BAM header, but was not in the provided FASTA file.”

Could anyone clarify how to properly use BAM files as input in RNAsplice?

Are there specific requirements for BAMs (e.g. transcriptome vs genome BAMs) or index compatibility that I should be aware of?

Any advice would be hugely appreciated — thank you so much in advance! 🙏

--source genome_bam

--transcript_fasta