Moderator: shenwei356
shenwei356 ♦ 5.2k
- Reputation:
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- http://shenwei.me/
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- shenwei356
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- Joined:
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Posts by shenwei356
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3
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... Try [seqkit grep](http://bioinf.shenwei.me/seqkit/usage/#grep)
seqkit grep -s -p "-" in.fa > out.fa ...
written 4 weeks ago by
shenwei356 ♦ 5.2k
0
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0
answers
133
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0
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... 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 6 weeks ago by
shenwei356 ♦ 5.2k
1
vote
0
answers
95
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0
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... 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 12 weeks ago by
shenwei356 ♦ 5.2k
1
vote
1
answer
88
views
1
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... grep -i -E '[^ACTGN]+' ...
written 12 weeks ago by
shenwei356 ♦ 5.2k
5
votes
6
answers
277
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6
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... 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 3 months ago by
shenwei356 ♦ 5.2k
4
votes
1
answer
218
views
1
answers
... [seqkit concat](http://bioinf.shenwei.me/seqkit/usage/#concat)
seqkit concat a.fasta b.fasta > c.fasta ...
written 3 months ago by
shenwei356 ♦ 5.2k
1
vote
3
answers
224
views
3
answers
... `seqkit subseq -r 1:20` is enough. ...
written 5 months ago by
shenwei356 ♦ 5.2k
1
vote
1
answer
192
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1
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... ```
# 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 6 months ago by
shenwei356 ♦ 5.2k
1
vote
3
answers
361
views
3
answers
... Learn some basic knowledge of SHELL: [I/O Redirection](http://linuxcommand.org/lc3_lts0070.php) ...
written 6 months ago by
shenwei356 ♦ 5.2k
3
votes
3
answers
361
views
3
answers
... 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 6 months ago by
shenwei356 ♦ 5.2k
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