This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Full length transcriptome from SRA data

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.

sra transcriptome
• 2,847 views • link
updated by Devon Ryan Devon Ryan • written by MAPK MAPK

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

Thank you, Devon. Very helpful information.

• 0 views • link
written by MAPK MAPK

Log in to answer this question.

More posts like this