I am trying to identify the unknown sequence of an gene from a plant species which has published RNAseq data deposited to SAR-NCBI.
As RNA seq data are all short read data, i am looking for an easy way to align the proper fragments together and find the whole sequence of that gene.
Thank you in advance
Mohammad
Hi Pritam,
Thank you so much for the link. It is really useful. Is the workflow suitable for the whole genome assembly or it can also be used to find only one gene (my case)?
Best regards
For de novo assembly of RNA-Seq data, I like Trinity. I've used it with both transcriptome and metatranscriptome data with great success.
https://github.com/trinityrnaseq/trinityrnaseq/wiki
You can use the trinotate pipeline to annotate your contig file to identify your gene or you can use blast to build a database from your contig file and search for your gene of interest.
If you have a reference gene, you can align the RNA-seq reads to your reference using bowtie2 and perform an assembly on only the reads that aligned to the gene.
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