Cucurbit Expression Atlas
RNA-Seq data analysis method
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 their 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 three mismatches. The resulting reads/read pairs were aligned to the corresponding genome using HISAT allowing up to two mismatches. Raw counts for each predicted gene were derived based on the alignments and then normalized to FPKM (fragments per kilobase of exon per million mapped fragments).
RNA-Seq collections
The cucurbit expression atlas database contains the following projects
Watermelon
![](/sites/default/files/img/fp_wm_s.png)
PRJNA209092
PRJNA221197
PRJNA338036
SRP012849
PRJNA270773
PRJNA319011
PRJNA326331
PRJNA328189
PRJNA389184
PRJNA416203
PRJNA422970
PRJNA454040
Cucumber
![](/sites/default/files/img/fp_cu_s.png)
PRJNA307098
PRJNA321023
PRJNA80169
PRJEB7612
PRJNA214462
PRJNA263870
PRJNA271595
PRJNA285071
PRJNA292785
PRJNA312872
PRJNA319011
PRJNA376073
PRJNA258122
PRJNA345040
PRJNA380322
PRJNA382994
PRJNA388584
PRJNA419665
PRJNA431940
PRJNA437579
PRJNA438923
PRJNA483118
Bottle gourd
![](/sites/default/files/img/bg_s.png)
PRJNA387615