Alignment For Paired End Fast Q Files To Use It For Samtools Mpileup

Question

[Deniz]

Hello,

My aim is looking for SNP and allele count differences between samples. I will use samtools mpileup to get a VCF file.

First, I used BOWTIE for alignment.

For single end fastq files

bowtie -S -q -p 8 -a --best -V2 -m 1 --strata Referans file.txt

How can I do it for paired end reads ? file1.txt and file2.txt

For Snp calling, I allowed 2 mismatches. Do you suggest any different command for alignment?

Thanks for any help.

[Rm]

http://samtools.sourceforge.net/mpileup.shtml

Answer 1

[Yumtaoist]

First of all, I think bowtie2 is better for the alignment of pair end reads.

The parameters can be set as:

bowtie2-align -x bt2-idx -1 file_1.txt -2 file_2.txt -S result.sam

Answer 2

[Ian]

You don't specify whether this is for Illumina or SOLiD reads. For SOLiD reads BFAST handles paired ends and uses SAM output.