Moderator: shenwei356

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shenwei3564.5k
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Posts by shenwei356

<prev • 541 results • page 2 of 55 • next >
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Comment: C: NCBI Species name with Taxonomy ID
... Just google and install GNU grep ~~ [How to install and use GNU Grep in OSX](https://apple.stackexchange.com/questions/193288/how-to-install-and-use-gnu-grep-in-osx) ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: NCBI Species name with Taxonomy ID
... Old one from ftp://ftp.ncbi.nih.gov/pub/taxonomy/. ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: NCBI Species name with Taxonomy ID
... Less than 1 second for me: ``` $ memusg -t grep -w -f species_taxids.txt scientific_names.txt > result.txt elapsed time: 0.893s peak rss: 177.77 MB $ wc -l * 2902963 names.dmp 2043416 nodes.dmp 1753136 result.txt 2043416 scientific_names.txt 1675766 species_taxids.txt 10418697 tot ...
written 12 weeks ago by shenwei3564.5k
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Answer: A: NCBI Species name with Taxonomy ID
... 1. Restrieving all taxids with rank of "species": $ awk '$5 == "species" {print $1}' nodes.dmp > species_taxids.txt $ head -n 3 species_taxids.txt 7 9 11 2. Taxids and theirs scientific names: awk -F $'\t' 'BEGIN {OFS="\t"} $7 == "scientific n ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: Finding 16 mer not present in GRCh38
... Good to hear that, mapping is the fastest and most scalable solution. ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: Finding 16 mer not present in GRCh38
... this answer had been deleted ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: How to separate sequences of two species from Metagenomics Analysis?
... Try mapping to E.coli first, check the coverage (they may share some genes), and assemble with unmapped reads. It may be hard to separate If they share some genes. ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: Finding 16 mer not present in GRCh38
... I found out 14-mers on my 48GB RAM PC, you can easily extend them to 16-mers. https://www.biostars.org/p/359420/#359449 .Email me if you need. shenwei356 at gmail ...
written 12 weeks ago by shenwei3564.5k
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Comment: C: Finding 16 mer not present in GRCh38
... A fast way to generate all k-mers for given k (k<=32) using [unikmer](https://github.com/shenwei356/unikmer): ``` # 4294967295 == ( 1<<(16*2) ) - 1 $ seq 0 4294967295 | unikmer decode -k 16 | head -n 3 AAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAC AAAAAAAAAAAAAAAG ``` FASTA format ``` $ seq 0 429496 ...
written 3 months ago by shenwei3564.5k
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Answer: A: How to generate a short sequence that does not align to the RefSeq?
... What's it for? 25 bp sequence not found in human genome? [A previous answer in another post](https://www.biostars.org/p/354468/#354787) suggested a good method by mapping k-mers to genome and filtering that not mapped. Here's a brute force method by myself: **counting smaller k-mers (k=14) in gen ...
written 3 months ago by shenwei3564.5k

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Appreciated 10 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 12 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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