Moderator: shenwei356

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shenwei3564.5k
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http://shenwei.me/
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Posts by shenwei356

<prev • 540 results • page 1 of 54 • next >
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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 20 hours ago by shenwei3564.5k
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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 21 days ago by shenwei3564.5k
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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 25 days ago by shenwei3564.5k
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Comment: C: How to best get ALL Bacterial proteins from NCBI
... You can also download `.faa.gz` files for every bacterium in [RefSeq](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria), check [another tutorial](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) ...
written 25 days ago by shenwei3564.5k
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Comment: C: Linearize fasta files
... ( ̄ へ ̄ )Yes, the [patch](https://github.com/lh3/seqtk/pull/123) is worth it. Thank you Fabian for this great patch! ...
written 5 weeks ago by shenwei3564.5k
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Answer: C: Linearize fasta files
... `seqtk seq input.fa` (1.3-r106 [68752fd](https://github.com/lh3/seqtk/commit/68752fd8497aff82b273b1f7f541b9905760586f)) is faster than `seqkit seq -w 0 input.fa` (v0.10.0) in my test on both SSD and HDD. Version: - seqkit [v0.10.0](https://github.com/shenwei356/seqkit/releases/tag/v0.10.0) - seqtk ...
written 5 weeks ago by shenwei3564.5k
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Comment: C: How to extract the last 1000 nt from a group of sequences in a FASTA file?
... [seqkit subseq](https://bioinf.shenwei.me/seqkit/usage/#subseq) supports this, if you want a fast solution. seqkit subseq -r -1000:-1 seqs.fa > result.fa If you want to learn programming, write some Python scripts using Biopython. ...
written 6 weeks ago by shenwei3564.5k
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Comment: C: How to get a FASTA file where you filter by length to exclude sortest and longes
... seems datamash can with `perc` operation. https://www.gnu.org/software/datamash/manual/datamash.html ...
written 7 weeks ago by shenwei3564.5k
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Comment: C: How to get a FASTA file where you filter by length to exclude sortest and longes
... It's simple: sorting by length, calculating q10 and q90, and retrieving seqs in this range. # Step 1 # Getting total number n=$(seqkit stats test.fa -T | sed 1d | cut -f 4) # Step 2, option A # "seqkit sort -l" needs unique headers. # "seqkit range" retrieve records in ...
written 7 weeks ago by shenwei3564.5k
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Comment: C: NCBI Species name with Taxonomy ID
... Just google and install GNU grep ~~ [How to install and use GNU Grep in OSX](https://apple.stackexchange.com/questions/193288/how-to-install-and-use-gnu-grep-in-osx) ...
written 8 weeks ago by shenwei3564.5k

Latest awards to shenwei356

Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 8 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: single line fasta to mult line fasta
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to get RNAfold (structure) output in text format
Scholar 5 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 6 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Appreciated 8 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Scholar 8 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Appreciated 8 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash
Teacher 8 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
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 10 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Appreciated 10 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

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