User: shenwei356

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shenwei3562.3k
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China
Website:
http://shenwei.me/
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shenwei356
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Google Scholar Page
Last seen:
4 hours ago
Joined:
4 years, 11 months ago
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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 • 310 results • page 1 of 31 • next >
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Comment: C: Difficulty using SPAdes - Error relating to access and specificity
... Read the manual carefully: http://spades.bioinf.spbau.ru/release3.10.1/manual.html#sec3.1 Example: spades.py -k 21,33,55,77 -t 12 -m 50 --careful -o outputdir -1 read_1.fq.gz -2 read_2.fq.gz ...
written 4 hours ago by shenwei3562.3k
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Comment: C: Interesting bioinformatics blogs (2017 edition)
... Thanks for sharing. Can you format them into an unordered list, that would be neater :) ...
written 19 hours ago by shenwei3562.3k
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Comment: C: statistic tools of Kmer including invalid character
... Would you please upvote/accept my answer if it helps and works. :) ...
written 4 days ago by shenwei3562.3k
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Comment: C: statistic tools of Kmer including invalid character
... A much much faster way by **pre-retrieving regions containing non-ACGT chars**. (SeqKit [v0.5.2-dev](https://github.com/shenwei356/seqkit/releases/tag/v0.5.2-dev) or later version needed). The result is a little different: `18,472,858 < 18,479,833`. But only 47s for genome chr1 now!!!! It will ...
written 4 days ago by shenwei3562.3k
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Comment: C: statistic tools of Kmer including invalid character
... 5.5 minutes on my laptop for human genome chr1 (~250 Mb, 248,956,422). It will take 67 hours for 200Gb data~. The bottle neck is that there are too many kmers :-P $ time seqkit head -n 1 dataset_B.fa \ | seqkit sliding -s 1 -W 33 \ | seqkit seq -s -w 0 \ | grep -c '[ ...
written 4 days ago by shenwei3562.3k
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Answer: A: statistic tools of Kmer including invalid character
... One way using [seqkit](http://github.com/shenwei356/seqkit), [download](https://github.com/shenwei356/seqkit/releases): $ echo -e ">seq\nANTTA" \ | seqkit sliding -s 1 -W 3 \ | seqkit grep -s -r -i -p '[^ACGT]' \ | grep -c '^>' 2 0. data source: FASTA format 1 ...
written 4 days ago by shenwei3562.3k
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Comment: C: statistic tools of Kmer including invalid character
... Is this a homework? Which way do you prefer, script or existed tools? Why do you want do this? If you'd like to write script, just sliding the sequences with window of `K` and step of `1`, and check every window (kmer) whether it contains non-`ACGT` characters. ...
written 4 days ago by shenwei3562.3k
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Comment: C: How to compare CDS gff with genome guided assembled gff
... I'm not familiar with RNAseq analysis. But according to your description, [bedtools2](https://github.com/arq5x/bedtools2) and [bedops](https://github.com/bedops/bedops) may help. gff can be converted to bed by [gff2bed](https://bedops.readthedocs.io/en/latest/content/reference/file-management/conver ...
written 5 days ago by shenwei3562.3k
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Comment: C: Order contig by size
... sort can be in reversed order: `sort -k1,1nr` ...
written 5 days ago by shenwei3562.3k
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Comment: C: Order contig by size
... oh right! didn't realize this. But it seems that OP wants rename contigs too. ...
written 5 days ago by shenwei3562.3k

Latest awards to shenwei356

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 6 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 11 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 11 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
Appreciated 13 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 13 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Appreciated 19 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Appreciated 25 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Appreciated 26 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 29 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 29 days 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
Voter 6 weeks ago, voted more than 100 times.
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
Teacher 10 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
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Scholar 11 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

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