Moderator: shenwei356

gravatar for shenwei356
shenwei3565.7k
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China
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http://shenwei.me/
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shenwei356
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Posts by shenwei356

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Comment: C: How to get the sequence differences between multiple bacterial genomes
... Yes, excluding similar sequences in human genome would be better. ...
written 7 weeks ago by shenwei3565.7k
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Answer: A: How to get the sequence differences between multiple bacterial genomes
... Here's one solution with [unikmer](https://github.com/shenwei356/unikmer), for limited number of input files. `for` loop can be replaced with `parallel` for saving time. 1. Generating k-mers. for f in *.fa.gz; do unikmer count -k 31 -K -s -o $f.k31 $f; done 2. Comp ...
written 7 weeks ago by shenwei3565.7k
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Comment: C: Search for sequence homology against various species
... Remote blastn, choose outfmt 6. ...
written 9 weeks ago by shenwei3565.7k
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Comment: C: Should we remove plasmid sequences for Whole genome Alignment
... Better remove them cause plasmids are highly mobile elements. ...
written 9 weeks ago by shenwei3565.7k
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Comment: C: Blastn on illumina reads for contamination detection before or after quality fil
... Blastn is very slow, you may use bwa o bowtie2 for mapping reads on known possible contamination genomes. Removing condamination AFTER QC is better, because the latter is faster. Runing the slower process in smaller data costs less time. ...
written 9 weeks ago by shenwei3565.7k
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Answer: A: Split Large Genome
... Try [seqkit sliding](https://bioinf.shenwei.me/seqkit/usage/#sliding), e.g., ``` $ echo -ne ">seq\nACTGGTCA\n" | seqkit sliding -s 3 -W 4 -g >seq_sliding:1-4 ACTG >seq_sliding:4-7 GGTC >seq_sliding:7-8 CA ``` For you, you need set the windows size as 10,000 with a step of 9900 ``` se ...
written 9 weeks ago by shenwei3565.7k
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Comment: C: Extract sequences from a list of ID
... Hmm... I've tested with your sample data, everything is OK. You may check the input data (check extra whitespace or tab at front/end of IDs, file encoding, even manually copy and search in the file with text editor.), and try with additional options, e.g., switch on `-i` to ignore cases. ...
written 12 weeks ago by shenwei3565.7k
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Comment: C: Extract sequences from a list of ID
... Option `-w` should be added to `grep` for exact matching. ...
written 12 weeks ago by shenwei3565.7k
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Answer: C: Extract sequences from a list of ID
... Referring to the [usage](https://bioinf.shenwei.me/seqkit/usage/#grep), you should not switch on `-n` , just use `seqkit grep -f id.txt seqs.fa`. -n, --by-name match by full name instead of just id -i, --ignore-case ignore case -r, --use-regexp pattern ...
written 12 weeks ago by shenwei3565.7k
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Answer: C: How to download all Pseudomonas aeruginosa Genomes from NCBI Genomes database?
... https://github.com/kblin/ncbi-genome-download or https://github.com/pirovc/genome_updater ...
written 12 weeks ago by shenwei3565.7k

Latest awards to shenwei356

Scholar 17 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Appreciated 17 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 12 weeks 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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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
Appreciated 8 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
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
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
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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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