Moderator: shenwei356

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shenwei3565.5k
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Posts by shenwei356

<prev • 579 results • page 1 of 58 • next >
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Comment: C: Extract sequences from a list of ID
... Hmm... I've tested with your sample data, everything is OK. You may check the input data (check extra whitespace or tab at front/end of IDs, file encoding, even manually copy and search in the file with text editor.), and try with additional options, e.g., switch on `-i` to ignore cases. ...
written 2 days ago by shenwei3565.5k
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Comment: C: Extract sequences from a list of ID
... Option `-w` should be added to `grep` for exact matching. ...
written 2 days ago by shenwei3565.5k
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Answer: C: Extract sequences from a list of ID
... Referring to the [usage](https://bioinf.shenwei.me/seqkit/usage/#grep), you should not switch on `-n` , just use `seqkit grep -f id.txt seqs.fa`. -n, --by-name match by full name instead of just id -i, --ignore-case ignore case -r, --use-regexp pattern ...
written 3 days ago by shenwei3565.5k
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Answer: C: How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?
... https://github.com/kblin/ncbi-genome-download or https://github.com/pirovc/genome_updater ...
written 6 days ago by shenwei3565.5k
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Comment: C: NCBI Viral Genomes Resource
... Just google with "NCBI Viral Genomes Resource", check the first result. ...
written 6 days ago by shenwei3565.5k
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Comment: C: Using Taxonomizr on R with a list of input.
... > I have a lot of inputs (around 7000) that i concatenante in .txt file like this Seems the one-line format is not the original format, one-name-per-line could be the easiest and most convenient for downstream processing. And 7000 is not a small number, you can try [taxonkit name2taxid](https: ...
written 6 days ago by shenwei3565.5k
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Comment: C: Using Taxonomizr on R with a list of input.
... You may [change the encoding of the text file](https://support.microsoft.com/en-us/office/choose-text-encoding-when-you-open-and-save-files-60d59c21-88b5-4006-831c-d536d42fd861) as `UTF8`. ...
written 7 days ago by shenwei3565.5k
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Comment: C: Using Taxonomizr on R with a list of input.
... You should show some lines of input .txt file at the very beginning. How may lines in it? df = read.csv("t.txt", quote="'", header=FALSE) species = as.vector(t(df[1, ])) # 1 means the first row. If there are more than one lines, use loop. ...
written 7 days ago by shenwei3565.5k
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Comment: C: Using Taxonomizr on R with a list of input.
... df = read.csv("C:/Users/pdoinel/Desktop/species.txt", header=FALSE) species <- as.vector(df[[1]]) data<-getId(species, taxaNames) ...
written 7 days ago by shenwei3565.5k
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Comment: C: Using Taxonomizr on R with a list of input.
... specieds <- as.list(read.csv("list.txt", header=FALSE)) data<-getId(specieds, taxaNames) ...
written 7 days ago by shenwei3565.5k

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Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
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