Hi, I'm using pileup to look for SNPs from bowtie alignment. There are several questions I wanna ask. Your help is greatly appreciated.
1. I observed the maximum SNP quality is 228. Is it correct?
2. $7 is always 60. What's wrong?
3. What does the symbol "$" or "^F" means in $8?
4. Will considering a SNPs site that are covered by reads from plus & minus strand reduce false positive?
5. Also, I noticed BWA maps less reads compared to Bowtie. It gives a lower mapping score, lower SNP quality score and thus, less SNPs. Can I trust these SNPs that are found in bowtie but not BWA alignment?
Cheers,
Melissa
1. I observed the maximum SNP quality is 228. Is it correct?
2. $7 is always 60. What's wrong?
3. What does the symbol "$" or "^F" means in $8?
4. Will considering a SNPs site that are covered by reads from plus & minus strand reduce false positive?
5. Also, I noticed BWA maps less reads compared to Bowtie. It gives a lower mapping score, lower SNP quality score and thus, less SNPs. Can I trust these SNPs that are found in bowtie but not BWA alignment?
Cheers,
Melissa
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