User: shenwei356

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shenwei3562.8k
Reputation:
2,780
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Location:
China
Website:
http://shenwei.me/
Twitter:
shenwei356
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Google Scholar Page
Last seen:
an hour ago
Joined:
5 years 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 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 • 360 results • page 1 of 36 • next >
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Comment: C: Blastp giving empty output file
... PLEASE click `ADD COMMENT` below answers to respond. ...
written 1 day ago by shenwei3562.8k
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Answer: A: Blastp giving empty output file
... These are lots of factors affecting the computation time: - BLAST database size. e.g., NCBI NR is very very big. - Query sequences size. - Parameters. - `-num_threads`. *You did not set `-num_threads`, which defines number of CPUs to use. I think this the main cause for your case.* - Computer ...
written 2 days ago by shenwei3562.8k
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Comment: C: A code for splitting FASTA file, No output is written for the file
... the loop logic for lines is not right. only one level is needed ...
written 5 days ago by shenwei3562.8k
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Comment: C: Blast standalone output formatting
... I suggest rerun the blast with outfmt 11, and convert it to any other outfmt (6 or 7) with `blast_formatter`. ...
written 6 days ago by shenwei3562.8k
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Answer: A: How to get total count of organisms with whole genome sequenced
... [I just counted the bacterial species with complete genomes](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) according to the ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt , it's `2517`. $ cat assembly_summary.txt | grep "Complete Genom ...
written 7 days ago by shenwei3562.8k
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Answer: A: how to select with unix a column by the column name in a txt files
... Using [csvtk](https://github.com/shenwei356/csvtk) or csvkit, or miller or xsv.... csvtk is a cross-platform, efficient, practical and pretty CSV/TSV toolkit in Golang. Hope you enjoy it. For a CSV file: $ cat 3.csv id,name,hobby 1,bar,baseball 2,bob,basketball 3,foo,football ...
written 7 days ago by shenwei3562.8k
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Comment: C: organism choose of clusterProfiler
... You can tag `clusterProfiler` to call the author [Guangchuang Yu](https://www.biostars.org/u/3039/) ...
written 9 days ago by shenwei3562.8k
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212
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Comment: C: Shortening fasta sequence names
... An "upvote" by clicking the "thumb up" picture at left of the answer is appreciated. ...
written 10 days ago by shenwei3562.8k
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Comment: C: shartening fasta sequence names
... Providing your failed commands could let people help to correct them. So you can improve your SHELL skills. ...
written 11 days ago by shenwei3562.8k
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212
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Answer: A: shartening fasta sequence names
... For Linux/Mac OS X, using shell command `sed` is the simplest way: # by removing "|" and later characters: sed -r 's/\|.+//' seqs.fa > newseqs.fa Since you asked `sed` command, please ignore method below: If you need to run on Windows, the simplest way is using [seqkit](http://bioinf ...
written 11 days ago by shenwei3562.8k

Latest awards to shenwei356

Scholar 9 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
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
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Scholar 23 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 28 days 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
Scholar 5 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 5 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 5 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 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
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
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
Appreciated 7 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Appreciated 7 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Appreciated 8 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 8 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 9 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Voter 10 weeks ago, voted more than 100 times.
Scholar 11 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

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