I aligned my sequence file to transcriptome sequence for chromosome 2 I downloaded from UCSC. I aligned it with bowtie2 and it seemed the alignment process was good without error. I ran eXpress software after that with the same Fasta file for aligning and the SAM result from the alignment as input. But, the eXpress software then gave an error about the length difference in a gene between FASTA file and SAM file. Can anyone help me? Thank you in advance for your help.