Negative vs positive strand of ssRNA se

Question

[ash]

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!

Answer 1

[Devon Ryan]

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.

[ash]

Thank you, Devon. That helps