Moderator: shenwei356

gravatar for shenwei356
shenwei3564.2k
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China
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http://shenwei.me/
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Posts by shenwei356

<prev • 493 results • page 1 of 50 • next >
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Comment: C: Merging all sequences with identical ID's
... please provide example. ...
written 14 days ago by shenwei3564.2k
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Comment: C: Find unique non overlapping intervals between two files?
... 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 shenwei3564.2k
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Answer: C: How do I replace the values in one file with the values in another file?
... 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 shenwei3564.2k
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Answer: C: Where can i get virus nt database for blastn?
... follow this https://bioinf.shenwei.me/taxonkit/tutorial/ ...
written 22 days ago by shenwei3564.2k
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Answer: A: So frustrated compiling necessary packages in a linux system
... you need bioconda: https://bioconda.github.io/ ...
written 29 days ago by shenwei3564.2k
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Comment: C: How to identify contigs containing the degenerate primer sequences using python?
... Oh, mismatch supported using the last version. ...
written 5 weeks ago by shenwei3564.2k
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Comment: C: Makeblast error when Nucleotide sequence contanis 'X" character
... 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 shenwei3564.2k
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Comment: C: How to extract reads that match k-mer profiles from a collection of sequences?
... https://github.com/will-rowe/hulk/ ? ...
written 5 weeks ago by shenwei3564.2k
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Comment: C: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in
... you need remove the leading symbol `@` by sed 's/^@//' id.txt > id2.txt ...
written 5 weeks ago by shenwei3564.2k
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Comment: A: How to identify contigs containing the degenerate primer sequences using python?
... (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 shenwei3564.2k

Latest awards to shenwei356

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 23 days ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 29 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Appreciated 4 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Appreciated 4 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: single line fasta to mult line fasta
Scholar 4 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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: 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
Scholar 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 6 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 6 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 9 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus

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