Comments (2)
The corresponding fields in blast output (q.start, q.end, s.start, s.end) return the starting and ending positions of the alignment, from the query or target point of view. For instance:
query: ACGT--
||
target: --GTCA
In that example, qlo = 3, qhi = 4, tlo = 1, thi = 2.
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Fixed in VSEARCH 0.1.0.
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Related Issues (20)
- Include rows of OTUs with no mapped reads in OTU tables
- EE: document the meaning of expected error values HOT 2
- appending sample names to fasta headers incomplete HOT 1
- Windows binaries: working with compressed files HOT 3
- --sizein seems having no effect in vsearch --usearch_global HOT 9
- Why FASTQ quality value above qmax is treated as Fatal error? HOT 5
- maxseqlength is not supported by makeudb_search command HOT 4
- Option to output the reason why merging failed
- Build errors with GCC 13 on Debian 13 HOT 8
- Too many "alignment score too low, or score drop too high" during pair-end merge compared with FLASH HOT 5
- fastq_mergepairs: merging stats should be written to log file if --log is used HOT 2
- add a DEBUG compilation option HOT 4
- Update log file output for --chimeras_denovo command HOT 1
- always report the rightmost match if multiple equivalent occurrences are present in target sequence? No. HOT 5
- compilation warning with ar: 'u' modifier ignored since 'D' is the default HOT 2
- sintax output is sometimes 4 columns and other times 5 columns HOT 3
- fastq_stripleft when the resulting length is null?
- forward read trimming and filtering (Minardi et al. 2021) HOT 1
- control of 2 separate randseed events in sintax HOT 10
- from fasta files to an OTU table HOT 1
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