I am trying to count aligned reads, using Salmon in alignment-based-mode
Command: salmon quant -t transcript.fa -l A -a accepted_hits.bam' -o salmon_quant
I am running into following error: " SAM file says target ENST00000618686.1 has length 228, but the FASTA file contains a sequence of length [2238 or 2237] "
I had generated transcript.fa from gffread.
Thanks in advance!!!!