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Moderator: shenwei356

gravatar for shenwei356
shenwei356 ♦ 4.9k
Reputation:
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China
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http://shenwei.me/
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shenwei356
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Google Scholar Page
Last seen:
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Joined:
7 years, 6 months ago
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http://shenwei.me/

Posts by shenwei356

<prev • 547 results • page 1 of 55 • next >
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Comment: C: How to get best DNA translation result?
... Try [seqkit translate --clean](https://bioinf.shenwei.me/seqkit/usage/#translate) ...
written 4 weeks ago by shenwei356 ♦ 4.9k
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Comment: C: How to concatenate multiple fasta file
... --id-regexp '^[^\|]+\|[^\|]+\|([^\|]+)\|' ...
written 5 weeks ago by shenwei356 ♦ 4.9k
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Answer: C: How can I add Sample Identifier to paired fastq file names
... try [brename](https://github.com/shenwei356/brename) ``` # read1 $ brename -f 'R1.+fastq$' -p _L -r '_S{nr}_L' -d [INFO] checking: [ ok ] 'Tube211-16S_L001_R1_001.fastq' -> 'Tube211-16S_S1_L001_R1_001.fastq' [INFO] checking: [ ok ] 'Tube212-16S_L001_R1_001.fastq' -> 'Tube212-16S_S2_L001_R1_0 ...
written 8 weeks ago by shenwei356 ♦ 4.9k
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Answer: C: How to subset fastq data based on leading nt of sequences?
... try [seqkit grep](http://bioinf.shenwei.me/seqkit/usage/#grep): seqkit grep -p '^NNNNNGGG' -d read_1.fq.gz -o out_1.fq.gz or seqkit grep -R 6:8 -p GGG read_1.fq.gz -o out_1.fq.gz ...
written 12 weeks ago by shenwei356 ♦ 4.9k
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Answer: A: How to match fasta header list of name?
... ``` # IDs in seqs.fa $ grep '^>' seqs.fa | awk '{print $1}' | sed 's/^>//' M.Bce12308ORF4755P M.Bce1254ORF9725P # IDs not in list.txt $ grep -w -v -f <(grep '^>' seqs.fa | awk '{print $1}' | sed 's/^>//') list.txt M.Bce122ORF1082P ``` ...
written 4 months ago by shenwei356 ♦ 4.9k
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Answer: C: Kill nohup bash process
... Hi, I'd recommend using [screen](https://linuxize.com/post/how-to-use-linux-screen/) instead of `nohup`, screen is safer. And, you better utilize some batch commands like `parallel` to accelerate thousands of jobs, here is `wget`. Using `wget -c` to resume unfinished download is also recommended. ...
written 5 months ago by shenwei356 ♦ 4.9k
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Comment: C: Determining total nucleotides for paired end metagenomic sequences
... Use [seqkit](https://github.com/shenwei356/seqkit) for saving time. seqkit stats xxxx_R[12].*.fastq.gz Results are something like these: ``` $ seqkit stats reads_*.fq.gz file format type num_seqs sum_len min_len avg_len max_len reads_1.fq.gz FASTQ DNA 2,500 567,516 ...
written 7 months ago by shenwei356 ♦ 4.9k
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Comment: C: Rename fasta-header based on a list
... Just for given sample data. ``` $ sed 's/^>//' headers.txt | perl -pne 's/(\w+_\w+)_/$1\t/' > headers.tsv $ cat headers.tsv NZ_CP023010 Elizabethkingia anophelis FDAARGOS_198 NZ_MRWY01000004 Klebsiella michiganensis_CAV1755 $ seqkit replace -p '^(.+?)\..+_' -k headers.tsv -r '{kv}_' ...
written 7 months ago by shenwei356 ♦ 4.9k
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Comment: C: Increase memory limit in SPAdes-3.6.1
... ``` $ spades.py --help SPAdes genome assembler v3.13.0 ... Advanced options: --dataset file with dataset description in YAML format -t/--threads number of threads [default: 16] -m/--memory RAM limit for SPAdes in Gb (terminat ...
written 8 months ago by shenwei356 ♦ 4.9k
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Comment: C: How to best get ALL Bacterial proteins from NCBI
... Yes I know, I guess proteins of bacteria in RefSeq are enough for his/her purpose, before knowing for what he/she use the data. Anyway, one can try ``` # downlaod wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt # reformat cat assembly_summary.txt | sed 1d | sed '1s/^# ...
written 8 months ago by shenwei356 ♦ 4.9k

Latest awards to shenwei356

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 11 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Popular Question 12 weeks 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 12 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 3 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 4 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 5 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Appreciated 9 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 9 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
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 12 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
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