User: hfan22

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hfan2230
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h*****@wisc.edu

Posts by hfan22

<prev • 12 results • page 1 of 2 • next >
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remote blast requires installation of taxdb database
... I was trying to do some remote blast. Here is my command: `blastn -query myquery.fasta -db nt -out myblast.out -remote -num_alignments 10 -outfmt "6 qacc saccver pident sscinames length mismatch gapopen evalue bitscore"` I wanted to get the scientific name instead of taxid so I requested sscina ...
blast written 22 months ago by hfan2230 • updated 11 weeks ago by Varshney20
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Comment: C: looking for a free command-line based quality score tool for sanger sequencing
... Sorry WouterDeCoster. I will follow the instruction next time. ...
written 2.1 years ago by hfan2230
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Comment: A: looking for a free command-line based quality score tool for sanger sequencing
... Thank you h.mon! Yes it's free for academic use. I should have read the Phred page more carefully (http://www.phrap.org/consed/consed.html#howToGet). Is there anything I could do to minimize future misunderstanding, like editing, or deleting my original post? I don't have a lot samples, 50-ish, but ...
written 2.1 years ago by hfan2230
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looking for a free command-line based quality score tool for sanger sequencing
... Dear all, I got some 16s (forward and reverse) sanger sequencing data (from ABI 3730xl DNA) from our on campus sequencing facility. They came in abi format but the quality scores have not been applied. When I asked for quality scores, the staff at the sequencing facility used KB Basecaller but also ...
fastq sanger sequencing abi quality score written 2.1 years ago by hfan2230
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Comment: C: Kover - order of metadata
... https://mega.nz/#F!n053zISY No key needed. kover commands used: kover dataset create from-tsv --genomic-data kmerMatrix.tsv --phenotype-name "rpoBsimulation" --phenotype-metadata metadata.tsv --output temp.kover kover dataset split --dataset temp.kover --id temp_split --train-size 0.666 --f ...
written 2.6 years ago by hfan2230
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Comment: C: Kover - order of metadata
... I thought so. But when I rearrange the order of the metadata (my metadata came in random order so I reordered them) the results are consistently different (same results for the same ordering but different for different ordering). I tried 4~5 version of the metadata (only vary by the order) and they ...
written 2.6 years ago by hfan2230
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Kover - order of metadata
... Hi Alex, Does the samples in the metadata should match with the order in the kmer matrix header? Supposedly I have a dumb dataset of 5 species: kmer matrix header: kmers t1 t2 t3 t4 t5 Metadata: t5 0 t1 1 t3 0 t2 1 t4 0 Will this cause any problem? ...
kover written 2.6 years ago by hfan2230 • updated 2.6 years ago by alexandre.drouin10
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Comment: C: kover installation problem: include could not find load file: GatbCore
... Thanks Alex. Yes that was exactly the problem. I was able to replicate the results from your example as well. Great documentation! Cheers, Huan ...
written 2.6 years ago by hfan2230
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Comment: C: kover installation problem: include could not find load file: GatbCore
... I thought I did! Isn't it besides the number of views? ...
written 2.6 years ago by hfan2230
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Comment: C: kover installation problem: include could not find load file: GatbCore
... The author of Kover. ...
written 2.6 years ago by hfan2230

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