Hi,
I have Illumina RNA single-end read data with 4 million sequences of read size 33 bases each. I used Velvet to perform de novo assembly on the RNA data. Velvet has generated contigs for the same. Since I come from computing background and has very little biology knowledge, I would appreciate if somebody can help me with the next steps. Does the output of velvet is final? What should be my confidence level looking at the contigs? What should do to verify/validate the output contigs? Should I use BLAST to find genes? Or can anybody suggest with a general pipleline that is followed to perform analysis post de novo assembly. Any help in this matter is greatly appreciated. Thank you.
I have Illumina RNA single-end read data with 4 million sequences of read size 33 bases each. I used Velvet to perform de novo assembly on the RNA data. Velvet has generated contigs for the same. Since I come from computing background and has very little biology knowledge, I would appreciate if somebody can help me with the next steps. Does the output of velvet is final? What should be my confidence level looking at the contigs? What should do to verify/validate the output contigs? Should I use BLAST to find genes? Or can anybody suggest with a general pipleline that is followed to perform analysis post de novo assembly. Any help in this matter is greatly appreciated. Thank you.
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