Full length transcriptome from SRA data

Question

[MAPK]

Hi,

I have 454 SRA data from NCBI and would like to get full length transcriptome and translate it to protein, how can I achieve this goal?

Thank you for your help.

Answer 1

[Devon Ryan]

Use a de novo assembler, such as trinity, and then write a script in biopython to find and translate the longest ORF in each contig. You could also blast the contigs in order to inform your choice of ORF, but that'd take longer.

[MAPK]

Thank you, Devon. Very helpful information.