Closed hermidalc closed 2 years ago
Hi @hermidalc,
The decoy sequence itself should be included at the end of the normal input reference fasta. The decoy file instead contains the names of the decoy records in the reference file. The error you are seeing is because its interpreting the fasta header as a name and that record isn't found in the normal reference file.
Ok thank you @rob-p that makes sense! Closing
I tried to load the latest GENCODE human genome FASTA as a decoy into pufferfish index and the
fixFasta
component immediately give the following error:Even though the genome file head looks like this:
I first thought it was the leading
N
s but even after clipping all leading and trailingN
s in all sequence entries it still gives the same error with the first sequence. It appears that when processing the decoy FASTA file fixFasta has a bug, because it doesn't notice the>
header(s).