Generation of Consenses Fasta from SAM/BAM
Dear All,
I have a SAM file which I got it from bwa mem (whole genome Data). My next step is to annotate the repeats using Repeat masker and to identify microstatellites using misa. For both MISA and Repeat Masker, I need fasta format. I tried to convert bam file to fasta format. But the result is not a continuous stretch of fasta. How can I get the continuous fasta file.
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mail2steff
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The term you are looking for is "assembly".
Ive found many posts dealing with
But I am not looking for any SNP or INDELS. Can I proceed with the same command?
What's wrong with the existing repeat masker annotation on your reference genome? If you sample is so different from your reference that the annotation isn't appropriate, why are you aligning to it in the first place?
I got only 60% of alignment percentage through bwa mem. My sample and reference are not so different. they belong to same species. Thats y I wanna find out microstatellites.