Question: Alignment For Paired End Fast Q Files To Use It For Samtools Mpileup
1
gravatar for Deniz
8.8 years ago by
Deniz210
Deniz210 wrote:

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.

paired samtools bowtie snp • 2.2k views
ADD COMMENTlink written 8.8 years ago by Deniz210

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

ADD REPLYlink written 8.8 years ago by Rm8.0k
3
gravatar for Yumtaoist
8.8 years ago by
Yumtaoist70
Yumtaoist70 wrote:

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

ADD COMMENTlink written 8.8 years ago by Yumtaoist70
0
gravatar for Ian
8.8 years ago by
Ian5.7k
University of Manchester, UK
Ian5.7k wrote:

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

ADD COMMENTlink written 8.8 years ago by Ian5.7k
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