Moderator: shenwei356
shenwei356 ♦ 5.7k
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- http://shenwei.me/
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- shenwei356
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Posts by shenwei356
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... Using GNU [datamash](https://www.gnu.org/software/datamash/) and [parallel](https://www.gnu.org/software/parallel/).
Sending every input line to `parallel`, which calls `sed` for converting space-delimited values to tab-delimited, and `datamash` for transposting column-wise data to row-wise, `sort ...
written 1 day ago by
shenwei356 ♦ 5.7k
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69
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... `seqkit grep -srip xxx` equals to `seqkit grep -s -r -i -p xxx`
$ seqkit grep -h
-s, --by-seq search subseq on seq, both positive and negative strand are searched, and mismatch allowed using flag -m/--max-mismatch
-r, --use-regexp patterns are regular ex ...
written 5 days ago by
shenwei356 ♦ 5.7k
1
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1
answer
264
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... [SPAdes](https://github.com/ablab/spades), definitely. ...
written 8 days ago by
shenwei356 ♦ 5.7k
0
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3
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3.0k
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3
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... Current version needs `-r`
```
bedtools flank -l 1000 -r 0 -i exons.bed -g hg38.txt > upstream.bed
``` ...
written 10 days ago by
shenwei356 ♦ 5.7k
1
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1
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154
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... Maybe they indeed share some sequences. You can check by mapping reads to mouse and rat ref seqs using [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) , blastn is too slow. ...
written 17 days ago by
shenwei356 ♦ 5.7k
0
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1
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160
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... @Biostar bot pushes this post to frontpage ~
It looks like a case of amplicon sequencing data, for retrieving amplicon from SE or merged PE reads. We did this a lot, so I wrote a tool [seqkit amplicon](https://bioinf.shenwei.me/seqkit/usage/#amplicon) (link for usage and examples) for these kind of ...
written 17 days ago by
shenwei356 ♦ 5.7k
5
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1
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179
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... I got a tool csvtk, the [uniq](https://bioinf.shenwei.me/csvtk/usage/#uniq) command can do exactly what you want , check the last example.
csvtk uniq -t -f 1 -n 5
The behind logic is easy, use a map/hash-table (column value -> count) to track how many times you have met a row with cerntain ...
written 18 days ago by
shenwei356 ♦ 5.7k
0
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128
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... see https://www.biostars.org/p/475263/ ...
written 4 weeks ago by
shenwei356 ♦ 5.7k
1
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2
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157
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2
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Answer:
A: Fasta file modification
... Try [seqkit mutate](http://bioinf.shenwei.me/seqkit/usage/#mutate).
$ echo -ne ">a\nATCG\n>b\ngcat\n"
>a
ATCG
>b
gcat
$ echo -ne ">a\nATCG\n>b\ngcat\n" | seqkit mutate -i -1:NNNN
[INFO] edit seq: a
[INFO] edit seq: b
>a
ATCGNNNN
...
written 6 weeks ago by
shenwei356 ♦ 5.7k
1
vote
1
answer
248
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1
answers
... Sorry, I just notice step 2 used the wrong command, and have edited the answer.
We should removing k-mers shared by >= 2 genomes (`unikmer common`), not just that shared by all genomes (`unikmer inter`). ...
written 7 weeks ago by
shenwei356 ♦ 5.7k
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For SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
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11 months ago,
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11 months ago,
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For A: looking for 16S RNA sequence consensus
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13 months ago,
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For A: looking for 16S RNA sequence consensus
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For A: How to get RNAfold (structure) output in text format
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For A: How to get RNAfold (structure) output in text format
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