Moderator: shenwei356
shenwei356 ♦ 4.2k
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Posts by shenwei356
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0
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1
answer
85
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1
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... please provide example. ...
written 14 days ago by
shenwei356 ♦ 4.2k
0
votes
1
answer
102
views
1
answers
... Try and explore [bedtools intersect](https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html) and [bedops](https://bedops.readthedocs.io/en/latest/) ...
written 17 days ago by
shenwei356 ♦ 4.2k
1
vote
3
answers
141
views
3
answers
... The strategy is straightforward:
1. reading file1 and save them in `map/hash/dict` with 4th column as keys,
2. and then read line in file2 one by one, replacing 1th and 2nd column with previous readed values from file1.
Here's a simple solution using [an unreleased version of csvtk](https://githu ...
written 17 days ago by
shenwei356 ♦ 4.2k
0
votes
1
answer
70
views
1
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... follow this https://bioinf.shenwei.me/taxonkit/tutorial/ ...
written 22 days ago by
shenwei356 ♦ 4.2k
6
votes
4
answers
300
views
4
answers
... you need bioconda: https://bioconda.github.io/
...
written 29 days ago by
shenwei356 ♦ 4.2k
0
votes
0
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206
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0
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... Oh, mismatch supported using the last version. ...
written 5 weeks ago by
shenwei356 ♦ 4.2k
0
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1
answer
96
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1
answers
... Replacing X with N. This should work.
seqkit replace -i -s -p X -r N in.fa.gz -o out.fa.gz ...
written 5 weeks ago by
shenwei356 ♦ 4.2k
0
votes
1
answer
167
views
1
answers
... https://github.com/will-rowe/hulk/ ? ...
written 5 weeks ago by
shenwei356 ♦ 4.2k
0
votes
1
answer
2.6k
views
1
answers
... you need remove the leading symbol `@` by
sed 's/^@//' id.txt > id2.txt ...
written 5 weeks ago by
shenwei356 ♦ 4.2k
0
votes
0
answers
206
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0
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... (Only for full match)
```
# positive strand
$ cat seqs.fa | seqkit grep -s -d -p NACTGN | seqkit seq -n -i | tee 1.txt
Contig4679
Contig4682
# negative strand
$ cat seqs.fa | seqkit seq -r -p | seqkit grep -s -d -p TTAM | seqkit seq -n -i | tee 2.txt
Contig4681
Contig4682
# intersection
$ csvtk i ...
written 9 weeks ago by
shenwei356 ♦ 4.2k
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For A: single line fasta to mult line fasta
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For A: single line fasta to mult line fasta
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For A: single line fasta to mult line fasta
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5 months ago,
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6 months ago,
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6 months ago,
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For A: single line fasta to mult line fasta
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6 months ago,
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9 months ago,
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