Hi all,
I made one consensus sequence using samtools, but need some clearness for the output. In my initial fasta file all bases are presented uppercase regardless if they are within exon, intron, etc. For the output I have:
nnnnnnnngagaacttCCCGCGnCCCGGCGGTnCCCAGCTCCNGGGnCCCCTAGcTCCAT
My target for sequencing was an intron, so I checked for match about gagaacttCCCGCG - lowercase matched to exon, uppercase matched to intron. But here I'm starting to guess - does N stands for a possible variant? What about n and c between the uppercase? Is there any documentation/rule about that? Thank you in advance.
I made one consensus sequence using samtools, but need some clearness for the output. In my initial fasta file all bases are presented uppercase regardless if they are within exon, intron, etc. For the output I have:
nnnnnnnngagaacttCCCGCGnCCCGGCGGTnCCCAGCTCCNGGGnCCCCTAGcTCCAT
My target for sequencing was an intron, so I checked for match about gagaacttCCCGCG - lowercase matched to exon, uppercase matched to intron. But here I'm starting to guess - does N stands for a possible variant? What about n and c between the uppercase? Is there any documentation/rule about that? Thank you in advance.