Cucurbit Expression Atlas

RNA-Seq analysis method description

The raw RNA-Seq reads were processed to remove adapters as well as low quality bases using Trimmomatic, and the trimmed reads shorter than 80% of original length were discarded. The remaining high-quality reads were aligned to the SILVA rRNA database to remove rRNA sequences using Bowtie allowing up to two mismatches. The resulting reads/read pairs were aligned to the corresponding genome using HISAT allowing up to two mismatches. The expression levels of transcripts were measured and normalized to FPKM (fragments per kilobase of exon per million mapped fragments) base on all mapped reads.

RNA-Seq collections

The cucurbit expression atlas database contains the following projects