I need to do assembly using a SRA entry of plant transcriptomic data. For example
SRA number "SRX5718892’ I need to do assembly. I am unable to do as it showing error every time. please tell me how to do Sequence assembly by transcriptomic data using SRA number
HI @Anand_Mishra,
firstly in order to perform the transcriptome assembly, it is necessary to select the samples corresponding to a specific specie; since the SRX5718892 includes transcriptomic data from two different Nepeta species, it is necessary to select a subset of sequences (e.g. Nepeta cataria samples). From this database entry, you can download the Accession List file. The next step is to upload that file to Galaxy by using the Uploader tool. Finally, you can use the Faster Download and Extract Reads in FASTQ format from the NCBI SRA tool to download the FASTQ datasets.
You can find a detailed explanation about how to perform the transcriptome assembly in the following link.
Regards