Hello, I am new to RNA-seq, and I have encountered an error with Salmon, with quantifying RNA-seq reads, and I would like some guidance as to what I should do.
I am working with Chicken RNA-seq reads and I have already aligned those reads to Gallus gallus GGRCg7b genome assembly, and generated transcriptome alignment with index generated from STAR.
I believe the index is generated from the genomic sequences? Not too sure how this affects the transcriptome alignments. When running Salmon on these alignments and using the transcripts fasta file from the genome assembly, I get the error that the sequence lengths do not match.
SAM file says target NM_001001193.1 has length 508, but the FASTA file contains a sequence of length [502 or 501]
Is there anything that went wrong with the process? Should I have just aligned the reads to transcripts or used different program, and was the genome alignment necessary/makes sense in this context?
Not too sure if I have to realign with transcripts with salmon or if there is anything that could be done, since the lengths are so similar.
I think this stems from an issue with the
STARaligner (refer here https://github.com/COMBINE-lab/salmon/issues/785 and links in there). You might want to try using a different aligner or, alternatively, try the solution(s) proposed in the thread I linked here.