Question: Generation of Consenses Fasta from SAM/BAM
0
gravatar for mail2steff
12 months ago by
mail2steff50
Potsdam, Germay
mail2steff50 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 • 464 views
ADD COMMENTlink written 12 months ago by mail2steff50
2

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 12 months ago by d-cameron2.0k

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 12 months ago by mail2steff50

The term you are looking for is "assembly".

ADD REPLYlink written 12 months ago by WouterDeCoster37k

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 12 months ago • written 12 months ago by mail2steff50
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