I want to ask what is the meaning of no. 1 of this explanation from eXpress website?
eXpress requires two input files:
A multi-FASTA file containing the transcript sequences. If the transcriptome of your organism is not annotated, you can generate this file from your sequencing reads using a de novo transcriptome assembler such as Trinity, Oases, or Trans-ABySS. If your organism has a reference genome you can assemble transcripts directly from mapped reads using Cufflinks. If your genome is already annotated (in GTF/GFF), you can generate a multi-FASTA file using the UCSC Genome Browser by uploading your annotation as a track and downloading the sequences under the "Tables" tab.
Read alignments to the multi-FASTA file in SAM or BAM format. These can either be stored in a file or streamed directly from an aligner. It is important that you allow as many multi-mappings as possible. You can also allow many mismatches during mapping since eXpress builds an error model to probabalistically assign the reads, although this will increase mapping time. If you are combining reads from several library preparations or from sequencing runs using different read lengths, please see the Manual for important details on how the alignments should be input.
I want to use human genome Hg38. I download the genome sequence in fasta format and gene annotation file in GTF format. I don't know what to do becuase it seems using these 2 files is not working for eXpress. In no. 1 also said I can upload to UCSC Genome Browser and download the sequences but I don't know how to do it. So, what file I should use for the multi-fasta file for no. 1? And besides that, can someone explaoin what is the difference between transcriptome sequence and genome sequence? Thank you in advance