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-   -   Need help about using IGV (http://seqanswers.com/forums/showthread.php?t=92586)

mhasandx 01-19-2020 02:53 AM

Need help about using IGV
 
Hello i am an undergraduate student from bangladesh. A senior brother want to find some mutation points. Like he chemically induced mutation on the mother plant (Rice plant ) and took 3 daughter mutant.
Now he has 4 sequence sorted BAM file , one mother plant and rest of three is mutant file.
Now he wants to know the mutation point on sequenced base points with the Refence Genome.
he uses IGV software (integrated genomics viewer) to find this manually. and save data on excel.
Example of alignment is here
https://i.imgur.com/FNWkH0l.png

But my question is there anysoftware there which can call this type of thing i want.
I calculated that is this is done manually it would take atlease 2years to complete the whole squence including 12 quantig.
SO if anyone knows please help me to solve this problem

chobeich 01-19-2020 11:13 PM

Hi,
"Now he wants to know the mutation point on sequenced base points with the Reference Genome"
That's called Variant Calling. Start from the beginning, google it!.
Once you understand what are you looking for and depending on you bioinformatics skills, you can choose from the different softwares abalible.

Americano 05-31-2020 11:27 PM

I never used this video format at all


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