Question: Generation of Consenses Fasta from SAM/BAM
gravatar for mail2steff
2.6 years ago by
Potsdam, Germay
mail2steff60 wrote:

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.

sam misa bam ngs fasta • 918 views
ADD COMMENTlink written 2.6 years ago by mail2steff60

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?

ADD REPLYlink written 2.6 years ago by d-cameron2.2k

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.

ADD REPLYlink written 2.6 years ago by mail2steff60

The term you are looking for is "assembly".

ADD REPLYlink written 2.6 years ago by WouterDeCoster44k

Ive found many posts dealing with

samtools mpileup -uf reference.fa aligment.bam | bcftools view -cg - | vcfutils vcf2fq

But I am not looking for any SNP or INDELS. Can I proceed with the same command?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by mail2steff60
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