Visualizing a specific gene in negative strand

[Nagarajan Raju]

Hi,

   I am wondering how to visualize a gene which is located in negative strand. For positive strand, I just entered the chromosome id: gene start position-gene end position in the search box and found the matching reads.  But not sure how to do this for gene in negative strand of the same chromosome. Please guide me

Thanks

[igv-help]

You do it the same way.   

[Nagarajan Raju]

Hi, thanks for the reply. This is protein coding gene and I have to convert the sequence into protein. For that, I have to reverse complement the consensus sequence, right? Also, when I generate consensus I am getting non-DNA nucleotides also (like S,M, etc). Is there any way I can get only DNA nucleotides?

Thanks

[igv-help]

Hi, thanks for the reply. This is protein coding gene and I have to convert the sequence into protein. For that, I have to reverse complement the consensus sequence, right?

This is not an IGV question,   I'm really not understanding what you are aking.

 

Also, when I generate consensus I am getting non-DNA nucleotides also (like S,M, etc). Is there any way I can get only DNA nucleotides?

Are you generating it from IGV?  No there is not,  you might want to look for more analysis oriented package to do this.     IGV is primarily for visualization.