User: shenwei356

gravatar for shenwei356
shenwei3561.4k
Reputation:
1,360
Status:
Trusted
Location:
China
Website:
http://shenwei.me/
Twitter:
shenwei356
Scholar ID:
Google Scholar Page
Last seen:
8 hours ago
Joined:
4 years, 9 months ago
Email:
s*********@gmail.com

Wei Shen is a PhD student of Microbiology studying Bioinformatic algorithm and gut metagenomics at Third Military University, China. He also tried to apply NGS technique to improve some molecular biology problems. More: Google ScholarResearchGate,ORCID.

He developed and share lots of reusable open-source tools of Bioinformatics and data manipulations at Github (also hosted at http://bioinf.shenwei.me). And he has written tens of posts about software development and scientific research. He also like to collect awesome resources on Bioinformatics, data science, machine learning and programming language, and share talks about Linux using and software development.

Posts by shenwei356

<prev • 158 results • page 1 of 16 • next >
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Comment: C: Short Blast with Gaps
... `seqkit locate -d`(http://bioinf.shenwei.me/seqkit/usage/#locate) can locate motif containing `N`, but it's exact not similar search. ...
written 3 days ago by shenwei3561.4k
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Answer: A: retrieve organism from protein list
... Target proteins from nr should have accesion id or gi, so 1. Mapping accession id or gi to taxid using [prot.accession2taxid.gz](ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz). [csvtk](http://bioinf.shenwei.me/csvtk/) is used for grepping given columns. $ zca ...
written 3 days ago by shenwei3561.4k
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Comment: C: combine fasta sequence
... In shell: Step 1) split sequences by FASTA header using [seqkit](http://bioinf.shenwei.me/seqkit/) seqkit split --id-regexp "\.(.+?)$" -i seqs.fa Step 2) combining sequences in a file to one sequence. for one splited file: $ echo ">ff" > combined.fa $ cat seqs.id_ff.fa | seqkit ...
written 4 days ago by shenwei3561.4k
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Comment: C: combine fasta sequence
... In R: `mutate` a ID column from name column, `group_by` ID column and `paste` sequence column. ...
written 4 days ago by shenwei3561.4k
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Answer: A: Combining two fasta sequences into one
... A solution using [seqkit](http://bioinf.shenwei.me/seqkit/), [csvtk](http://bioinf.shenwei.me/csvtk/) and shell `sed`. Sample files (**not in same order**, **can be multiple lines**): $ cat 1.fa >seq1 aaa aa >seq2 ccc cc >seq3 ggg gg $ cat 2.fa ...
written 8 days ago by shenwei3561.4k
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Comment: C: How to merge two csv tables
... updated: [v0.4.5](https://github.com/shenwei356/csvtk/releases/tag/v0.4.5) ...
written 8 days ago by shenwei3561.4k
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Comment: C: How to merge two csv tables
... omg, I figure out before falling asleep! just change the order of files: csvtk --tabs join --fields 1 --keep-unmatched 1.csv 2.csv and use `csvtk -t cut -f 1,4,5,2,3` to reorder columns. good night ...
written 8 days ago by shenwei3561.4k
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Comment: C: How to merge two csv tables
... Sorry, it does not support this feature. Since more than one user need this, I'll add this soon. ...
written 8 days ago by shenwei3561.4k
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Answer: A: How to merge two csv tables
... Although you want to solve this by Python script, there are some CSV/TSV tools can easily achieve this, including [csvtk](https://github.com/shenwei356/csvtk), [csvkit](http://csvkit.readthedocs.io/en/749/), [xcv](https://github.com/BurntSushi/xsv) and [miller](https://github.com/johnkerl/miller). ...
written 9 days ago by shenwei3561.4k
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Answer: A: How to run BWA or the other aligner for paired .fastq in a bash loop and pipelin
... For some files: a_1.fq.gz a_2.fq.gz b_1.fq.gz b_2.fq.gz Use glob for PE read1, and replace the suffix to get the sample name. for f in *_1.fq.gz; do r1=$f; r2=${f/_1.fq.gz/}._2.fq.gz; echo $r1 $r2; # do somethings done Result: a_1.fq.gz a._2.fq.g ...
written 10 days ago by shenwei3561.4k

Latest awards to shenwei356

Teacher 8 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 12 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Scholar 13 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Guru 4 weeks ago, received more than 100 upvotes.
Scholar 4 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Centurion 6 weeks ago, created 100 posts.
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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 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
Supporter 4 months ago, voted at least 25 times.
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
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

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