Moderator: shenwei356

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shenwei3564.4k
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Posts by shenwei356

<prev • 520 results • page 1 of 52 • next >
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Comment: C: Passing a file to sed to remove all lines that match +1 in file B from file A
... Just use `seqkit seq -n -i seqs.fa ` to retrieve IDs. ...
written 5 days ago by shenwei3564.4k
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Comment: C: Extract all bacteria sequences from the nr database
... [BLAST+ 2.8.1 with blastdb v5](https://ncbiinsights.ncbi.nlm.nih.gov/2019/01/04/blast-2-8-1-with-new-databases-and-better-performance/) allow you to limit your search by taxonomy using information built into the BLAST databases. So you don't need to build blastdb for specific taxids now ! ...
written 10 days ago by shenwei3564.4k
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Answer: A: removed entrie sequence include specific letters
... Try [`seqkit grep`](https://bioinf.shenwei.me/seqkit/download/) ([usage](https://bioinf.shenwei.me/seqkit/usage/#grep)). seqkit grep -i -s -r -p '[zxb]' -v # cat test.fa | seqkit grep --ignore-case --by-seq --use-regexp --pattern '[zxb]' --invert-match # seqkit grep -i -s -p z -p ...
written 13 days ago by shenwei3564.4k
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Comment: C: removed entrie sequence include specific letters
... Will you remove sequences containing `J`? ``` A Ala Alanine B Asx Aspartic acid or Asparagine [2] C Cys Cysteine D Asp Aspartic Acid E Glu Glutamic Acid F Phe Phenylalanine G Gly Glycine H His Histidine I Ile Isoleucine J Isoleucine or Leucine [4] K Lys Lysine L Leu Leucine M Met Meth ...
written 13 days ago by shenwei3564.4k
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Comment: C: Designing a primer from reads
... As you tagged, you should assemble the genome or target sequence region firstly, before designing primers. Actually, I have no idea about what you want. ...
written 13 days ago by shenwei3564.4k
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Comment: C: multiple DNA file Sliced to a fixed length substring by index/location
... It seems like a homework, or [XY Problem](http://xyproblem.info/). You should at least tell us what have you tried, or why do you want to this, what's the original purpose. ...
written 13 days ago by shenwei3564.4k
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... I can send nr.3041.fa.gz (70M) to you via email, if you give my address or write email to me. ...
written 24 days ago by shenwei3564.4k
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... Well, I tried 3041, and every step worked fine. $ wc -l $id.taxid.txt 9703 3041.taxid.txt $ wc -l $id.acc.txt 383332 3041.acc.txt $ pigz -dc nr.$id.fa.gz | grep '^>' -c 383332 $ time makeblastdb -parse_seqids -in nr.$id.fa -dbtype prot -out nr.$id Building a ne ...
written 24 days ago by shenwei3564.4k
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Comment: C: how to find a region of sequence based on region
... checking is id2head.tsv blank. if it is, paste result of seqkit seq -n df1.fa | head -n 5 | cat -A if not, paste result of head -n 5 id2head.tsv | cat -A ...
written 24 days ago by shenwei3564.4k
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... please paste results of wc -l 3041.taxid.txt wc -l 3041.acc.txt I'll check it on monday. ...
written 25 days ago by shenwei3564.4k

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Teacher 29 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
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