• Assessing the Read Content of the Transcriptome Assembly
• First, build a bowtie2 index for the transcriptome:
• Then perform the alignment to just capture the read alignment statistics.
• Visualize statistics:
• Visualize read support using IGV
• Sort the alignments by coordinate
• Index the coordinate-sorted bam file
• Index the Trinity.fasta file
• View the aligned reads along the Trinity assembly reference contigs.