I am using express 1.5.1 to calculate the read counts for RNA Seq data. I have removed rRNA contamination from the raw data and I am using the reads to map the reference genome GRCh37. When I run express tool, it throws the following error:
WARNING: Could not connect to update server to verify current version. Please check at the eXpress website (http://bio.math.berkeley.edu/eXpress). WARNING: Target 'ENST00000335137.3|ENSG00000186092.4|OTTHUMG00000001094.1|OTTHUMT00000003223.1|OR4F5-001|OR4F5|918|CDS:1-918|' exists in MultiFASTA but not alignment (SAM/BAM) file.
The command I am using is as follows:
express gencode.v19.pc_transcripts.fa tophat_out/accepted_hits.rmdup.bam --output-dir . --calc-covar
I understand from the error message that the transcript file I am using for quantification does not match with the alignment BAM file reference information. I am using the same reference genome file here. Does this step require me to map the reads to the transcript fasta before I do the quantification step? Any help would be highly appreciated.