Question: Negative vs positive strand of ssRNA se
0
gravatar for ash
4.3 years ago by
ash0
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 4.3 years ago • written 4.3 years ago by ash0

Thank you, Devon. That helps

ADD REPLYlink written 4.3 years ago by ash0
0
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k 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 4.3 years ago by Devon Ryan90k
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