Moderator: shenwei356

gravatar for shenwei356
shenwei3564.0k
Reputation:
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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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6 years, 3 months ago
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Posts by shenwei356

<prev • 461 results • page 2 of 47 • next >
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Comment: C: Split sequence according the 'N' base
... Another way producing same result of yours. ``` seqkit locate -P -p '[^Nn]+' seqs.fa --gtf > contigs.gtf seqkit subseq --gtf contigs.gtf seqs.fa | sed -r 's/_.+//' | seqkit rename | seqkit seq -i ``` ...
written 5 weeks ago by shenwei3564.0k
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Answer: A: Blast many sequences
... You need [taxonomic profiling softwares](https://omictools.com/taxonomy-dependent2-category), like [Kraken](https://ccb.jhu.edu/software/kraken/) and [Kaiju](https://github.com/bioinformatics-centre/kaiju) . BLAST is the slowest for this kind of task. ...
written 6 weeks ago by shenwei3564.0k
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Comment: C: Mapping columns based on a list
... Answer updated. It's much easier. ...
written 6 weeks ago by shenwei3564.0k
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Comment: C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in
... How about outputting sequence lengths and ploting using other tools $ seqkit fx2tab hairpin.fa -l | csvtk cut -t -f 4 | csvtk plot hist -H > hist.png ![image](https://image.ibb.co/ePLKQ8/t.png) Or ``` # https://github.com/derwiki/histogram $ seqkit fx2tab hairpin.fa -l | csvtk cut -t -f 4 ...
written 6 weeks ago by shenwei3564.0k
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Comment: C: Mapping columns based on a list
... run ./csvtk xxx ...
written 6 weeks ago by shenwei3564.0k
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Comment: C: Mapping columns based on a list
... it supports mac. https://github.com/shenwei356/csvtk/releases/download/v0.13.0/csvtk_darwin_amd64.tar.gz ...
written 6 weeks ago by shenwei3564.0k
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Answer: A: Mapping columns based on a list
... Try [csvtk](https://github.com/shenwei356/csvtk), supporting the two files are tab-separated. **updated** with [v0.14.0](https://github.com/shenwei356/csvtk/releases/tag/v0.14.0) or later version ``` ./csvtk rename2 -t -f -gene -p '(.+)' -r '{kv}' -k <(./csvtk cut -t -f 2,1 barcodes.tsv) -K o ...
written 6 weeks ago by shenwei3564.0k
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Comment: C: Remote some IDs from IDs list
... Taking one day to learn some shell knowledge can save you much time. Finding Things: http://swcarpentry.github.io/shell-novice/07-find/index.html ...
written 6 weeks ago by shenwei3564.0k
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Answer: A: Remote some IDs from IDs list
... You need [learn some basic shell commands](https://github.com/swcarpentry/shell-novice), like `grep`. You need this for this post: grep -v -f small.txt big.txt > big-small.txt And what's the most important, try **provide enough information when asking problem. Providing some sample data ca ...
written 6 weeks ago by shenwei3564.0k
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Comment: C: Remove sequence from fasta file by samtools
... seqkit grep -v -f ID-list.txt seqs.fa ID-list.txt: one ID per line. ...
written 6 weeks ago by shenwei3564.0k

Latest awards to shenwei356

Appreciated 10 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Commentator 10 days ago, created a comment with at least 3 up-votes. For C: 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
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 19 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 25 days 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
Teacher 6 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
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Teacher 9 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
Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 11 weeks 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
Popular Question 5 months ago, created a question with more than 1,000 views. For csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
Appreciated 7 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 10 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 10 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 13 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

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