I'm trying to correct a Pacbio assembly performed with CANU. The idea is to perform a first correction round with Pacbio reads using Arrow (3 iterations), in order to correct SNPs, following with Pilon and Illumina reads to fix indels (5 itarations, my coverage is around 25-fold). I also have RNA-seq data which I may use. To monitor the behaviour of the whole process I map onto each iteration the Genomic illumina reads and RNA-seq reads.
This is what happens:
This is the mapping for the genomic reads
And this is for the RNA.
Of course the effect is higher in the DNA reads because it's more extended.
What I found weird, and I don't know how to explain it the effect of the Arrow first and Pilon after. There a substantial increase of multiple mapping with arrow with a strong decrease when pilon is used.
Is that normal?
The other question I have is: am I doing right in correcting only indels with Pilon? Should I also correct SNPs and maybe using RNA data to only corrent indels?
Hi,
I'm trying to correct a Pacbio assembly performed with CANU. The idea is to perform a first correction round with Pacbio reads using Arrow (3 iterations), in order to correct SNPs, following with Pilon and Illumina reads to fix indels (5 itarations, my coverage is around 25-fold). I also have RNA-seq data which I may use. To monitor the behaviour of the whole process I map onto each iteration the Genomic illumina reads and RNA-seq reads.
This is what happens:
This is the mapping for the genomic reads
Of course the effect is higher in the DNA reads because it's more extended.
What I found weird, and I don't know how to explain it the effect of the Arrow first and Pilon after. There a substantial increase of multiple mapping with arrow with a strong decrease when pilon is used.
Is that normal?
The other question I have is: am I doing right in correcting only indels with Pilon? Should I also correct SNPs and maybe using RNA data to only corrent indels?
Thank for your help F