Hello, Thanks in advance for any help!
I have RNAseq data from a dozen or so individuals assembled to a reference transcriptome using CLC and wish to end up with a fasta set of contigs for each individual which includes degenerate bases where appropriate. Ive been using samtools and dont seem to have any problems there, except the fasta (or fastq) output has lost any degenerate bases... As far as i can tell Im using samtools correctly (theres even an example in the manual for how to 'generate the consensus for one diploid individual') but even changing the parameters i cant get any degenerate bases. If someone has done this I would really appreciate some help! Thanks again,
I have RNAseq data from a dozen or so individuals assembled to a reference transcriptome using CLC and wish to end up with a fasta set of contigs for each individual which includes degenerate bases where appropriate. Ive been using samtools and dont seem to have any problems there, except the fasta (or fastq) output has lost any degenerate bases... As far as i can tell Im using samtools correctly (theres even an example in the manual for how to 'generate the consensus for one diploid individual') but even changing the parameters i cant get any degenerate bases. If someone has done this I would really appreciate some help! Thanks again,