How to use BBmap (mutate.sh) to simulate the human genome?
Hi! I want to simulate the human genome. I found a suitable BBMap mutate.sh) program. The mutate.sh only outputs reads that contain mutations. But I need to get a fast output file that would contain reads with mutation and without mutations. I want to try to maintain the coverage of the reference genome. How can i do this?
Now I use the command to run:
1.bbmap/mutate.sh in=reference/gh19.fasta out = reference/hg19_with_mut.fasta id = 0.99 prefix = bbmap
I can use the program BBMap randomreads.sh) , but it looks much more difficult to run and I'm afraid to unconsciously get an undesirable result
• 1,584 views
•
link
updated
by
Biostar
•
written
by
kamanovae •
•
written
by
kamanovae •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Mapping to a template sequece
written by QX •
-
BWA align in human and parasite genome, and sort them
written by Bender •
-
randomreads.sh adding abundances for metagenomic like distribution
written by eozcan •
-
False positive adaptor findings on FastQC/MultiQC using BBMaps randomreads.sh
written by GLR •
-
BBMap tool error - randomreads.sh
written by GLR •
-
randomreads.sh simulated reads dont map to genome
written by grant.hovhannisyan
-
paired-end reads in BBMap randomreads.sh
written by grant.hovhannisyan
-
Generate artificial reads
written by finswimmer
-
Nucleotide coverage if >5 reads
written by Vca80553 •
-
To Simulate Heterozygous Variations In Genome
written by Pascal
One does not really simulate a genome but you simulate reads using the reference for that genome.
randomreads.shis not difficult to run.Do you need to simulate a genome at this point? There are plenty available in databases. You can run
mutate.shon one of them to introduce the mutations, if you don't want to simulate a new dataset.At this stage, I need to introduce mutations in the reference genome, and then I plan to use the NanoSim program to simulate nanopore reads. My final goal is nanopore reads with introduced mutations. Which program is better for the first step?
Then use
mutate.sh.Take a look at processing parameters to control the mutations.