![]() ![]() Different linkage evidences have unique estimated lengths table2asn –indir path_to_fsa_files -t template -M n -Z –gaps-min 10 –gaps-unknown 100 -l align-genusģ.When there are both estimated length and unknown length gaps with the same linkage evidence and the unknown length gaps are a single unique length, you need to include -l for the linkage evidence, -gaps-unknown for the length of runs of N's that represent unknown length gaps, and -gaps-min for the minimum runs of N's to convert to estimated length gaps.Įxample: if runs of 10 or more N's are estimated gaps, and shorter runs of N's are just ambiguous bases, and all runs of exactly 100 N's are unknown gaps, and the linkage evidence is align-genus: Both estimated length and unknown length gaps are present You will need to check your assembly parameters to determine what the N's represent. Do not add assembly_gaps for single or short runs of N's that represent ambiguous bases. Note that you should only include an assembly_gap for runs of N's that represent gaps. table2asn -indir path_to_fsa_files -t template -M n -Z –gaps-min 5 -l paired-ends.Similarly, if every N represents an estimated length gap, use -gaps-min 1.Įxample: Every run of 5 or more Ns represents a gap of estimated length, and the linkage evidence is paired-ends: For example, if all of the gaps are estimated length (there are no unknown length gaps) and runs of 5 or more N's are estimated gaps and shorter runs of N's are ambiguous bases, then use -gaps-min 5. Use –gaps-min to indicate the minimum run of N's to be converted to an estimated length gap. Different linkage evidences have unique estimated lengths.Both estimated length and unknown length gaps are present.linkage-evidence-file : to call a 2-column file of gap lengths and their linkage evidences when gaps of specific lengths have different linkage evidences align-trnscpt (ie, the evidence is a transcript).paired-ends (ie, for paired ends or mate pairs, eg from Illumina or PacBio). ![]() These are the available options (they correspond to the options for column 9 of an AGP file): l (lowercase 'l' as in 'linkage') : type of evidence used to assert linkage across the gaps.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |