User: jmartin77777

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Posts by jmartin77777

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Comment: A: Extract 10 matches in BLAST
... If you are running ncbi blastn from the command line you can limit the number of results displayed per query using the -num_descriptions (or possibly its -num_alignments ... one controls the one-line summaries and the other controls the ascii alignment views that are output in the default format). ...
written 22 months ago by jmartin777770
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Help fixing issue with genbank submission (FeatureBeginsOrEndsInGap)
... I've submitted an annotated assembly to GenBank and after their review they found some problems I need to address. These annotations are on a draft assembly, contigs organized into scaffolds. The annotation was done using MAKER on the scaffold fasta file. The problem GenBank has pointed out is t ...
annotation submission written 22 months ago by jmartin777770 • updated 21 months ago by Biostar ♦♦ 20
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Comment: A: Per position amino acid frequency from mapping short reads vs. long coding ampli
... Thats worth a try. I'm concerned about whether tools will correctly handle a sam file with protein alignments, but if it works that would be what I need! ...
written 2.3 years ago by jmartin777770
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Per position amino acid frequency from mapping short reads vs. long coding amplicon
... I need to build a table of amino acid frequencies per position along a ~900 amino acid amplicon that is all coding, based on the alignment of 1-2 million illumina 100mers to that amplicon. I'm trying to emulate results I've done before, but in that earlier case I had PacBio long reads that each m ...
alignment written 2.4 years ago by jmartin777770

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