I'm just learning how to use blast from the command line. I used blastn to search contigs in our genome assembly against a local database of the chicken genome. I ran two separate runs one with -outfmt 0 (pairwise) and -outfmt 7 (tabular with comment lines).
What I would like to do is extract the dna alignments of each query and subject sequence and put these in a file with query and subject sequence ids. Becuase I am very new to blast from the command line I have two questions:
(1) Instead of extracting the pairwise alignments from the outfmt 0 and sequence ids from outfmt 7, would it be easier to make some custom blast command that returns both pieces of information in one database? If so any suggestions on how to do this?
(2) Results from both blast runs only show numbers (e.g. 20) for the subject sequence ids matching to our assembly in the chicken genome. The fasta formatted chicken assembly I am using does have a separate .gff file that does have subject sequence ids, but I can't figure out how to add the .gff file to the chicken blast database I made. I don't think the makeblastdb command supports .gff files so I don't know how to extract the subject ids from this. Any ideas you have are greatly appreciated.