User: shenwei356

... 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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Comment: C: How to get the target sequence of matching consensus motif using Seqkit?

... `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

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Answer: C: What is the best way to assemble Illumina paired end reads?

... [SPAdes](https://github.com/ablab/spades), definitely. ...

written 8 days ago by shenwei356 ♦ 5.7k

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Comment: C: retrieve 1000 bp upstream sequences

... 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

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154

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Comment: C: How to check if a Fastq file is contaminated with other strains?

... 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

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Answer: C: Select sequences if contain two specific substrings

... @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

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Answer: C: Get the top X number of lines per unique value in one column, once you've sorted

... 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

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128

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Comment: C: How to identify specific region using Mauve?

... see https://www.biostars.org/p/475263/ ...

written 4 weeks ago by shenwei356 ♦ 5.7k

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157

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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

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Comment: C: How to get the sequence differences between multiple bacterial genomes

... 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

Latest awards to shenwei356

Scholar 18 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

Appreciated 18 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

Scholar 9 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

Appreciated 9 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

Scholar 12 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

Popular Question 3 months ago, created a question with more than 1,000 views. For csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit

Appreciated 3 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

Great Question 6 months ago, created a question with more than 5,000 views. For SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Appreciated 8 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

Popular Question 8 months ago, created a question with more than 1,000 views. For SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

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 9 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

Popular Question 10 months ago, created a question with more than 1,000 views. For SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Appreciated 10 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

Teacher 11 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

Appreciated 11 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

Teacher 11 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

Scholar 13 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format

Teacher 15 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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