User: shenwei356

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shenwei3563.6k
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http://shenwei.me/
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Posts by shenwei356

<prev • 438 results • page 2 of 44 • next >
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Comment: C: Renaming fasta headers according to a matching name list
... Firstly preparing the mapping file of accession and GI: If you have Unix/Linux, it's simple: ``` paste <(seqkit seq -n -i seqs.fasta) gi.txt AFA46815.1 222528058 AFA46816.1 222528059 AFA46817.1 222528060 ``` If not, you may need help of [csvtk](http://bioinf.shenwei.me/seqkit/do ...
written 5 weeks ago by shenwei3563.6k
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Answer: A: sorting an alignment in fasta format after the tip order in a phylogenetic tree
... Using fasta index. If the ID list is not long, simply paste the IDs into cmd. samtools faidx seqs.fasta $(paste -s -d " " ids.txt) > result.fasta Or seqkit faidx seqs.fasta $(paste -s -d " " ids.txt) > result.fasta For large number of IDs: cat ids.txt | parallel -k seqkit fa ...
written 7 weeks ago by shenwei3563.6k
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Answer: A: How to read a loop over to read a file in a folder for many folders
... Try [easy_qsub](https://github.com/shenwei356/easy_qsub) for easily submitting multiple PBS jobs. For a cluster, tt's better than submitting one job which handles multiple files. easy_qsub 'echo {} > {}.out' dir/*.fq.gz ...
written 11 weeks ago by shenwei3563.6k
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Answer: A: grep a column based on a string
... Try [`csvtk`](https://github.com/shenwei356/csvtk), ([usage](http://bioinf.shenwei.me/csvtk/usage/#cut) of `csvtk cut`). For tab-delimited file: `t.tsv` ``` $ cat t.tsv sample gene17 gene92 gene1 gene20000 patient1 0.03569654 1.020565 0.003652 0.25247236 patient2 ...
written 12 weeks ago by shenwei3563.6k
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Comment: C: find identical sequences with different header
... The result indeed is the `>NP_000009.1`. Don't you check the out.fasta? ...
written 12 weeks ago by shenwei3563.6k
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Answer: A: find identical sequences with different header
... seqkit common --by-seq --ignore-case file1.fasta file2.fasta file3.fasta > out.fasta [Download binaries](http://bioinf.shenwei.me/seqkit/download/) for Linux/Windows/Mac OS X, [usage](http://bioinf.shenwei.me/seqkit/usage/#common) ...
written 12 weeks ago by shenwei3563.6k
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Answer: A: How do I normalize this data for plotting?
... Here's a way in `R` using `dplyr` and `tidyr`, only data of one sample is processed. ``` library(dplyr) library(tidyr) library(ggplot2) # for plot # library(gglogo) # for plot df <- read.csv("SampleA.tsv", sep = "\t", header = FALSE) df <- t(df) # transpose colnames(df) <- ...
written 3 months ago by shenwei3563.6k
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Answer: A: split fasta of a protein sequence into consecutive n amino acids
... There are many methods. For long terms, some programming skill is worth learning. Here's a simple way by using [seqkit](http://bioinf.shenwei.me/seqkit/usage/#sliding). $ seqkit sliding -s 1 -W 8 seqs.fa >albumin_sliding:1-8 MKWVTFIS >albumin_sliding:2-9 KWVTFISL ... ...
written 3 months ago by shenwei3563.6k
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Comment: C: Renaming FASTA headers while keeping some previous information?
... seqkit replace -p "^(.+?) " -r "\${1}{nr} " seqs.fa ...
written 3 months ago by shenwei3563.6k
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Comment: C: Extract all bacteria sequences from the nr database
... nucl_gb.accession2taxid.gz ...
written 5 months ago by shenwei3563.6k

Latest awards to shenwei356

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 5 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 5 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
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 5 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 11 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 11 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 12 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 12 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 12 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 12 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 12 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

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