User: shenwei356

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shenwei3561.6k
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China
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http://shenwei.me/
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shenwei356
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Last seen:
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4 years, 10 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 • 215 results • page 1 of 22 • next >
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Answer: A: Color code protein sequence alignment result to a reference sequence in black an
... Try [Jalview](http://www.jalview.org/) ...
written 34 minutes ago by shenwei3561.6k
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Answer: A: Add sequence lengths to headers in a fasta file
... [seqkit](http://bioinf.shenwei.me/seqkit/download/) + awk on Linux/OS X cat seqs.fa | seqkit fx2tab --length | awk -F "\t" '{print $1"["$4"]\t"$2}' | seqkit tab2fx > seqs2.fa Example $ echo -e ">seq\nacgtn\nACGTN" >seq acgtn ACGTN $ echo -e ">seq\nacgtn\nA ...
written 12 hours ago by shenwei3561.6k
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Answer: A: Producing the Reverse-complement of each sequence in fastq files
... You may try [seqkit](http://bioinf.shenwei.me/seqkit/download/) (**v0.4.5 or later**, run `seqkit version` to check version), which *provides executable binary files for Linux/Windows/OS X. Just download, decompress and immediately use.* $ seqkit seq t.fq.gz @K00137:236:H7NLVBBXX:6:1126:2 ...
written 20 hours ago by shenwei3561.6k
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Answer: A: how to rearrange fasta file according to its length
... Sorting by seq length using [seqkit](https://github.com/shenwei356/seqkit): $ seqkit sort -l hairpin.fa Filtering by seq length ([usage](http://bioinf.shenwei.me/seqkit/usage/#fx2tab-tab2fx) of `seqkit fx2tab` and `seqkit tab2fx`): $ seqkit fx2tab -l hairpin.fa | awk -F "\t" '$4 >= 100 ...
written 23 hours ago by shenwei3561.6k
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Comment: C: What are lowercase a,t,c,g refer to in a complete genome? Should lower case a,t,
... https://www.biostars.org/p/93706/ ...
written 6 days ago by shenwei3561.6k
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Comment: C: Match, count and extract the positions of exact strings of nucleotides from mult
... alright. i get it. i get it ...
written 7 days ago by shenwei3561.6k
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Comment: C: Match, count and extract the positions of exact strings of nucleotides from mult
... I'm a little confused, we just need change the regular expressions. Your `AG*2` in regular expression is `(AG){2}`, `A*3` is `A{3}`. `[^AG]` at the start and end of `[^AG][AG]{6}[^AG]` is redundant. You may want `(AG){6}`. ...
written 7 days ago by shenwei3561.6k
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Comment: C: Match, count and extract the positions of exact strings of nucleotides from mult
... just use regular expression I mentioned above, e.g., `[AG]{6,}`, `[AT]{6,}`. ...
written 7 days ago by shenwei3561.6k
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Comment: C: Match, count and extract the positions of exact strings of nucleotides from mult
... You may change the motifs (regular expression), e.g. ``` $ cat motifs.fa >As A{3,} >Ts T{3,} >ATs [AT]{6,} ``` ``` $ seqkit locate -P -f motifs.fa *.fasta \ | csvtk -t sort -k patternName -k seqID -k start \ | csvtk -t pretty seqID patternName pattern strand start en ...
written 7 days ago by shenwei3561.6k
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Comment: C: Match, count and extract the positions of exact strings of nucleotides from mult
... What's your original purpose? It does looks like a homework. If not, you can write a tiny script in Perl/Python to fulfill your special out format. [`seqkit locate`](http://bioinf.shenwei.me/seqkit/usage/#locate) can do similar job but the output format is a little different. ``` $ seqkit locate ...
written 8 days ago by shenwei3561.6k

Latest awards to shenwei356

Scholar 11 hours ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 11 hours ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 9 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Voter 14 days ago, voted more than 100 times.
Scholar 18 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 6 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Scholar 6 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Guru 9 weeks ago, received more than 100 upvotes.
Scholar 9 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Centurion 10 weeks ago, created 100 posts.
Teacher 12 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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 3 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

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