When I run samtools with follow parameters:
samtools mpileup -C50 -Q25 -q1 -l %s -f %s %s
I got a output as follow:
21 34124586 G 38 ,,,,AAA,AAAAa..,,,aaa.AaA,,A,,aaaaaaaA
From samtools manual:
"At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a ’>’ or ’<’ for a reference skip, ‘ACGTN’ for a mismatch on the forward strand and ‘acgtn’ for a mismatch on the reverse strand."
How can I see 'A' at the forward strand, then see 'A' at the reverse strand?
From the result, at position chr21:34124586, it seems it is heterozygous snp A/G. If the gene is expressed on the forward strand. So we should only see A or G on the forward strand. Why it can mapped to the reverse strand. Because only the forward strand DNA has been transcript to mRNA. The reverse strand does not.
I am a bit of confused here. Could any one give me some hits?
Thank you very much in advance.
samtools mpileup -C50 -Q25 -q1 -l %s -f %s %s
I got a output as follow:
21 34124586 G 38 ,,,,AAA,AAAAa..,,,aaa.AaA,,A,,aaaaaaaA
From samtools manual:
"At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a ’>’ or ’<’ for a reference skip, ‘ACGTN’ for a mismatch on the forward strand and ‘acgtn’ for a mismatch on the reverse strand."
How can I see 'A' at the forward strand, then see 'A' at the reverse strand?
From the result, at position chr21:34124586, it seems it is heterozygous snp A/G. If the gene is expressed on the forward strand. So we should only see A or G on the forward strand. Why it can mapped to the reverse strand. Because only the forward strand DNA has been transcript to mRNA. The reverse strand does not.
I am a bit of confused here. Could any one give me some hits?
Thank you very much in advance.
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