Hi All,
I have a bam file with ssRNA-Seq data. I was viewing it using bamview.
I blasted one of the both positive and negative strand sequences on NCBI using blast and gives a positive strand result for both. For positive read beginning of the gene and for the negative read at the end of the gene. I get the position but shouldn't the reverse strand read be +/- when blasted?
Could anyone please explain?
Thank you so much!
1 answer
A BAM file always stores sequences and positions oriented to the + strand. If a read is mapped to the - strand, the reverse complement sequence is stored. This is quite convenient, since the POS field is always the left-most position of the sequence and the sequence always extends 5'->3' along the + strand.
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Devon Ryan
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