Tweet
I'm using SOAPsnp to identify SNP. Is there any visualization for SOAPsnp pileup?
Thanks, guys.
Thanks, guys.
-
-
What exactly do you want to visualize? If think you want to see the mapped reads and where they differ from reference (known/possible SNPs) as stacked output (so all complete reads!)... If so you should use mapping output to visualize that. For example SAM/BAM format in IGV, you will see all mapped reads stacked on top of the reference sequence. See links:Originally posted by sukhbat View Post
For SOAP I see there is a soap2sam converter (perl script):
http://soap.genomics.org.cn/
In IGV you can load and view SAM/BAM:
http://www.broadinstitute.org/igv/
Or try some other NGS viewer, for a software comparison:
http://lh3lh3.users.sourceforge.net/NGSalnview.shtml -
Thanks man!Comment
-
Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
Comment