Moderator: shenwei356

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shenwei3565.2k
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China
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http://shenwei.me/
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Posts by shenwei356

<prev • 557 results • page 1 of 56 • next >
3
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Answer: C: Extract Sequences from Multiple sequence alignment containing special character
... Try [seqkit grep](http://bioinf.shenwei.me/seqkit/usage/#grep) seqkit grep -s -p "-" in.fa > out.fa ...
written 3 months ago by shenwei3565.2k
0
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0
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182
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0
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Comment: C: Please help me finding the best match of the primer sequence from the multi fast
... try [seqkit locate](http://bioinf.shenwei.me/seqkit/usage/#locate) for searching primers, and seqkit amplicon for extracting amplicon with primers, both commands allow mismatch. ...
written 3 months ago by shenwei3565.2k
1
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0
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Comment: C: lineage analysis on microbial samples (tuberculosis)
... Try QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data , https://doi.org/10.1186/s12864-020-6486-3 , https://github.com/AbeelLab/quanttb/ ...
written 5 months ago by shenwei3565.2k
1
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1
answer
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1
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Answer: C: Finding non ATCGN nucleotides in a fasta file?
... grep -i -E '[^ACTGN]+' ...
written 5 months ago by shenwei3565.2k
5
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6
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369
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6
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Answer: A: How to rename multiple fastq files
... Lots of solution from others work, but I'd like to recommend a **safer** solution of mine ([brename](https://github.com/shenwei356/brename/)), in case you overwrite files with others by accident, which is common in batch renaming files using regular expression. brename checks all operations befor ...
written 5 months ago by shenwei3565.2k
4
votes
1
answer
267
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1
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Answer: A: How to concatenate clustalw aligned fasta sequence?
... [seqkit concat](http://bioinf.shenwei.me/seqkit/usage/#concat) seqkit concat a.fasta b.fasta > c.fasta ...
written 6 months ago by shenwei3565.2k
1
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3
answers
266
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3
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Comment: C: Extract N amino acids from fasta file
... `seqkit subseq -r 1:20` is enough. ...
written 7 months ago by shenwei3565.2k
1
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1
answer
243
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1
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Answer: C: Merging 3 files based on first column
... ``` # converting to tab-delimited $ ls *.txt | parallel 'csvtk space2tab {} > {.}.tsv' # all possible values in 1th column $ cut -f 1 *.tsv | sort | uniq | tee 0.tsv # join together $ csvtk join -H -t -k -t *.tsv --fill - A 1 3 6 B 2 3 - C 5 - ...
written 8 months ago by shenwei3565.2k
1
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3
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408
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3
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Comment: C: merge multiple files by commom column names
... Learn some basic knowledge of SHELL: [I/O Redirection](http://linuxcommand.org/lc3_lts0070.php) ...
written 8 months ago by shenwei3565.2k
3
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3
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408
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Answer: A: merge multiple files by commom column names
... A solution using [`parallel`](https://www.biostars.org/p/63816) and [`csvtk`](https://github.com/shenwei356/csvtk): ``` # converting space-delimited to tab-delimited l$ s *.txt | parallel 'csvtk space2tab {} > {}.tsv' # retrieving colnames $ ls *.txt.tsv | parallel 'csvtk headers -t {} | csvtk ...
written 8 months ago by shenwei3565.2k

Latest awards to shenwei356

Appreciated 10 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
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: How to get RNAfold (structure) output in text format
Appreciated 5 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 5 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Appreciated 5 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 7 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 11 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
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Appreciated 11 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format

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