Question: Tajima'S D Test-Ngs Data
1
gravatar for jackuser1979
7.0 years ago by
jackuser1979860
US
jackuser1979860 wrote:

I have RNA seq illumina paired-end reads mapped to reference genome using bowtie and have bam file from samtools. I am interested in calculateing Tajima's D test using DNAsp. As DNAsp software accepts FASTA file, I have converted bam file into fasta format.

samtools view filename.bam | \awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fas

I have Imported this converted fasta file into DNAsp for Neutrality-based statistical test. Does this conversion and doing calculation is correct way of doing or I should do multiple alignment using clustal to get fasta file?

ADD COMMENTlink modified 7.0 years ago • written 7.0 years ago by jackuser1979860
1

I don't think you can compute a TD with just the reads, you need to generate a modified sequence with your variants and then compute the TD comparing with your original reference.

ADD REPLYlink written 7.0 years ago by JC8.7k

Why not? If the reads are aligned to the reference using bowtie & samtools, we get aligned file in bam format just like clustal alignment.

ADD REPLYlink written 7.0 years ago by jackuser1979860

Yes, it seems to me that DNAsp needs aligned complete sequences to perform the TD test... check the manual. BTW, the problem will be the same when using tools like PAML...

ADD REPLYlink written 7.0 years ago by Bioch'Ti1000

I'm just wondering how to generate the modified sequence with the variant from NGS dat, I mean VCF/AM/reference mapping file. Any idea ?

ADD REPLYlink written 7.0 years ago by Bioch'Ti1000
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