I am working on comparative transcriptome analysis; having two different genotype of same plant species. I have come across soapSNP (linux based package). Is there any other window based or linux based software to perform SNP identification ?
I hope this link will be useful for you. There are many tools available for analyzing transcriptomics data
https://omictools.com/transcriptomics-category
Dear Ankush,
In addition to soapSNP you can use the following tools:
1) MAQ (http://maq.sourceforge.net/).
2) Samtools (http://www.htslib.org/doc/samtools.html)
3) SNPEff (http://snpeff.sourceforge.net/SnpEff_manual.html)
4) SNPSift (http://snpeff.sourceforge.net/SnpSift.html#Extract)
MAQ and Samtools are the most commonly used for SNP calling. I can provide scripts for identification SNP sites for aforementioned tools if you need.
Dear Olha,
Thanks for your kind response. It would be really great if you can provide script for this analysis.
Mail I'd : [email protected]
Thank you again.
Hi Ankush,
You may want to check out GATK's best practices document for variant calling in RNA-seq data: https://software.broadinstitute.org/gatk/guide/article?id=3891
Good luck!
I am giving you some general example. Check the application in your work.
Windows based is - QualitySNPng
Linux based are provided by other users which are great but check FREEBAYES. It might be useful too.
Still I would suggest you to use Linux based.
Best
Pal
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Software