We have performed denovo assembly for the pig species. Now we are interested in checking the percentage of assembly mapped over reference available in NCBI. I know BWA can do this but not able to figure out how? Please share your experience I will be grateful to you all.
I would recommend
QUAST – Quality Assessment Tool for Genome Assemblies
I tried using QUAST and it gave me a report of GC%, N50, N75, L50, L75 which we already found. Is there any way we can tell how much % of the reads mapped to contigs of reference genome? or Genome Coverage. Any lead will be of great help. Thanks..!!
quest does exactly that, you have the plot for the genome coverage, etc
basically it generates substantially more information beyond just an N50 stat,
usually you don't even need Quast for N50 as the assembler itself produces that information
Found the solution for above mention thread.
After indexing I followed the following steps:
bwa mem -M -R "TAG" pig.fa ref.fa > mapped.sam
samtools view -bS mapped.sam > mapped.bam
Bam files was later sorted:
samtools sort mapped.bam mapped_sort.bam
indexed this file:
samtools index mapped_sort.bam
Run flagstat to find the desired mapping results:
samtools flagstat mapped_sort.bam > mappingat.txt
This text file will have your results saved.
I agree my post was not exactly clear. I tried to explain but gone in different direction. I will try to pinpoint the issue from now onwards. Thanks
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