User: shenwei356

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shenwei3563.2k
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Location:
China
Website:
http://shenwei.me/
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shenwei356
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Last seen:
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Joined:
5 years, 4 months ago
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Wei Shen is a PhD student of Microbiology studying Bioinformatic algorithm and gut metagenomics at Third Military University, China.

He develops and shares many reusable open-source tools on Bioinformatics and data manipulations on Github (http://bioinf.shenwei.me). And he also likes writing posts on software development and scientific research.

Learn more: Google Scholar | ResearchGate | ORCIDGithub.

Posts by shenwei356

<prev • 393 results • page 2 of 40 • next >
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Comment: C: fasta file to tab delimited file
... [seqkit](https://github.com/shenwei356/seqkit) seqkit tab2fx xxx.tab > xxx.fasta ...
written 11 weeks ago by shenwei3563.2k
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Answer: A: I have DNA motifs 6-12 bp long. Trying to get conservation measurements for them
... For locating motifs, try `locate` command ([usage](http://bioinf.shenwei.me/seqkit/usage/#locate)) of [SeqKit](https://github.com/shenwei356/seqkit). For some motifs: $ cat motifs.txt ACTNGCT GCTGRTCGAAC Convert to FASTA format which seqkit wants: $ awk '{print ">"$1"\n"$1}' ...
written 11 weeks ago by shenwei3563.2k
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Answer: A: Pattren counter in fasta file
... You can also try [SeqKit](https://github.com/shenwei356/seqkit). $ seqkit locate -p CAGAT seqs.fa | column -t seqID patternName pattern strand start end matched chr1 CAGAT CAGAT + 6 10 CAGAT chr1 CAGAT CAGAT + 24 28 CAGAT ch ...
written 11 weeks ago by shenwei3563.2k
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Answer: A: Fetching NCBI ID for a list of species?
... try [taxonkit](https://github.com/shenwei356/taxonkit), providing single binary files for Windows/Linux. It's really fast. $ cat names.txt Homo sapiens Akkermansia muciniphila ATCC BAA-835 Akkermansia muciniphila Mouse Intracisternal A-particle Wei Shen uncultured murin ...
written 11 weeks ago by shenwei3563.2k
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Comment: C: extracting sequences from a fasta file
... this script needs python2, you ran using py3. ...
written 3 months ago by shenwei3563.2k
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Comment: C: extracting sequences from a fasta file
... it's a regular expression for matching "gene:xxxxx", 、`[^ ]+` is for gene id consisting of non-space characters, and seqkit has to use `()` to capture the xxx as FASTA ID. ...
written 3 months ago by shenwei3563.2k
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Comment: C: Any tool designed to align short reads to long reads?
... that would be no sense,cause the reference is error-prone. ...
written 3 months ago by shenwei3563.2k
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Comment: C: extracting sequences from a fasta file
... above solution should work. ...
written 3 months ago by shenwei3563.2k
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Answer: C: extracting sequences from a fasta file
... An easy way provided by [seqkit](https://github.com/shenwei356/seqkit): seqkit grep -f ids.txt --id-regexp "gene:([^ ]+)" seqs.fa Cause the ID you want to search is in the FASTA description not the regular FASTA ID. SeqKit provides way to specify where the ID is by regular expression. `"ge ...
written 3 months ago by shenwei3563.2k
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Comment: C: extracting sequences from a fasta file
... so, are the list gene names? ...
written 3 months ago by shenwei3563.2k

Latest awards to shenwei356

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 10 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 10 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 4 months 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
Scholar 4 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Scholar 4 months 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
Scholar 4 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 5 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 5 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 5 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Appreciated 5 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

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