This is my first time working with RNA data. So far, I've run the dataset through trimmomatic, sortmeRNA, megahit and BWA. I'm trying to run Salmon using the SAM file output from BWA and the .fa resulting from megahit as the transcriptome.
I run this line:
./salmon-1.8.0_linux_x86_64/bin/salmon quant -p 12 -t Sample1_megahit.contigs.fa -l A -a Sample1_megahit.annotation_bwa.sam -o Sample1_salmon
I get this error at the end of a stream of lines that all say a variation of "this transcript not found in reference" and I'm not sure what reference it's referring to: Please provide a reference FASTA file that includes all targets present in the BAM header.
Should I be passing the unassembled transcriptome from before megahit or something? The megahit file filtered to have only transcripts that had successful BWA alignments? I'm not sure how to do that. The data was originally paired end, if that is relevant.
Thanks in advance!