Moderator: shenwei356

gravatar for shenwei356
shenwei3565.0k
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http://shenwei.me/
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Posts by shenwei356

<prev • 553 results • page 1 of 56 • next >
3
votes
7
answers
179
views
7
answers
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 6 days ago by shenwei3565.0k
4
votes
1
answer
129
views
1
answers
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 20 days ago by shenwei3565.0k
1
vote
3
answers
185
views
3
answers
Comment: C: Extract N amino acids from fasta file
... `seqkit subseq -r 1:20` is enough. ...
written 10 weeks ago by shenwei3565.0k
1
vote
1
answer
137
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1
answers
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 12 weeks ago by shenwei3565.0k
1
vote
3
answers
304
views
3
answers
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 3 months ago by shenwei3565.0k
3
votes
3
answers
304
views
3
answers
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 3 months ago by shenwei3565.0k
0
votes
0
answers
148
views
0
answers
Comment: C: How to get best DNA translation result?
... Try [seqkit translate --clean](https://bioinf.shenwei.me/seqkit/usage/#translate) ...
written 4 months ago by shenwei3565.0k
1
vote
4
answers
2.2k
views
4
answers
Comment: C: How to concatenate multiple fasta file
... --id-regexp '^[^\|]+\|[^\|]+\|([^\|]+)\|' ...
written 4 months ago by shenwei3565.0k
1
vote
3
answers
251
views
3
answers
Answer: C: How can I add Sample Identifier to paired fastq file names
... try [brename](https://github.com/shenwei356/brename) ``` # read1 $ brename -f 'R1.+fastq$' -p _L -r '_S{nr}_L' -d [INFO] checking: [ ok ] 'Tube211-16S_L001_R1_001.fastq' -> 'Tube211-16S_S1_L001_R1_001.fastq' [INFO] checking: [ ok ] 'Tube212-16S_L001_R1_001.fastq' -> 'Tube212-16S_S2_L001_R1_0 ...
written 5 months ago by shenwei3565.0k
5
votes
2
answers
255
views
2
answers
Answer: C: How to subset fastq data based on leading nt of sequences?
... try [seqkit grep](http://bioinf.shenwei.me/seqkit/usage/#grep): seqkit grep -p '^NNNNNGGG' -d read_1.fq.gz -o out_1.fq.gz or seqkit grep -R 6:8 -p GGG read_1.fq.gz -o out_1.fq.gz ...
written 6 months ago by shenwei3565.0k

Latest awards to shenwei356

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 6 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Appreciated 8 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 20 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 9 weeks 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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Teacher 4 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
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Appreciated 6 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Popular Question 6 months ago, created a question with more than 1,000 views. For csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
Appreciated 6 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 7 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
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Teacher 10 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta

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