Question: Negative vs positive strand of ssRNA se
gravatar for ash
5.0 years ago by
United States
ash0 wrote:


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!




ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by ash0

Thank you, Devon. That helps

ADD REPLYlink written 5.0 years ago by ash0
gravatar for Devon Ryan
5.0 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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.

ADD COMMENTlink written 5.0 years ago by Devon Ryan94k
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