Hey guys,
I need to assemble a genome de novo. Unfortunately I got Illumina SE50bp data (I know, worst case...). Coverage is approx. 20 - 25 so not as bad as it could be. However further on i got some transcritome data from the same organism which is also Illumina PE95bp reads. Now I am thinking of using this transcriptome data to improve the de novo genome assembly.
As I am thinking of it a first shot workflow would look like:
Assemble SE50bp DNA reads with SoapDenovo into contigs.
Assemble PE95bp cDNA reads with SoapDenovo-trans (to stay in a closed form, say) into contigs.
Try to improve contigs from DNA-seq with RNA-seq conitigs via CAP3, for instance.
But the problem i got is, does it make sense at all to try. Sure more data isn't bad at all but the RNA-seq is not mentioned to be support data at all.
What's your opinion?
Thanks in advance for your post.
Best,
Phil
I need to assemble a genome de novo. Unfortunately I got Illumina SE50bp data (I know, worst case...). Coverage is approx. 20 - 25 so not as bad as it could be. However further on i got some transcritome data from the same organism which is also Illumina PE95bp reads. Now I am thinking of using this transcriptome data to improve the de novo genome assembly.
As I am thinking of it a first shot workflow would look like:
Assemble SE50bp DNA reads with SoapDenovo into contigs.
Assemble PE95bp cDNA reads with SoapDenovo-trans (to stay in a closed form, say) into contigs.
Try to improve contigs from DNA-seq with RNA-seq conitigs via CAP3, for instance.
But the problem i got is, does it make sense at all to try. Sure more data isn't bad at all but the RNA-seq is not mentioned to be support data at all.
What's your opinion?
Thanks in advance for your post.
Best,
Phil
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