Moderator: shenwei356

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shenwei3564.1k
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Posts by shenwei356

<prev • 484 results • page 2 of 49 • next >
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Answer: A: Custom nr database with only arthropods ?
... ***Do not follow this answer.*** Here's the whole commands (replacing `pigz` with `gzip` if `pigz` not installed). id=6656 # Step 1) list all taxid below $id taxonkit list --ids $id --indent "" > $id.taxid.txt # Step 2) get all accessions # 3 min for me ...
written 8 days ago by shenwei3564.1k • updated 7 days ago by genomax55k
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Comment: C: Custom nr database with only arthropods ?
... I'll check it after a full download of nr.gz. And have to go to work now. ...
written 9 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... change seqkit grep -f virus.taxid.acc.txt nr.gz -o nr.virus.fa.gz to ``` zcat nr.gz \ | perl -e 'BEGIN{ $/ = ">"; <>; } while(<>){s/>$//; $i = index $_, "]\n"; $h = substr($_, 0, $i)."]"; $s = substr $_, $i+2; while($h =~ /(.+?) \[(.+?)\]/g){ print ">$1 [$2]\n$s";} } ...
written 9 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... what's the taxid are you using? ...
written 10 days ago by shenwei3564.1k
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Comment: C: Custom nr database with only arthropods ?
... [Extract all protein sequences of specific taxons from the NCBI nr database](https://bioinf.shenwei.me/taxonkit/tutorial/#extract-all-protein-sequences-of-specific-taxons-from-the-ncbi-nr-database), and `makeblastdb`. ...
written 15 days ago by shenwei3564.1k
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Comment: C: Delete all files with a pattern.
... for loop, check pattern using grep, check the $?, 0 means found, then you can delete it. ...
written 4 weeks ago by shenwei3564.1k
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Comment: C: How to concatenate multiple fasta file
... Please show REAL example ASAP. $ for f in *.fa; do seqkit replace -p '^(.+?)-(.+)$' -r '$1 $2' $f > f.$f; done $ seqkit concat f.*.fa ...
written 4 weeks ago by shenwei3564.1k
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Comment: C: How to concatenate multiple fasta file
... Here's an example: $ cat mix.fa >My_bacteriaA GeneA a >My_bacteriaA GeneB c >My_bacteriaB GeneA g >My_bacteriaB GeneB t Step 1. spliting by custom IDs $ seqkit split --id-regexp "^.+ (.+?)$" -i mix.fa -f -O out [INFO] split by ...
written 5 weeks ago by shenwei3564.1k
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Answer: C: How to concatenate multiple fasta file
... # split species and genes $ for f in *.fa; do seqkit replace -p '^(.+)_(.+?)$' -r '$1 $2' $f > f.$f; done $ seqkit seq -n f.GeneA.fa My_bacteriaA GeneA My_bacteriaB GeneA My_bacteriaC GeneA # concatenate seqs by IDs $ seqkit concat f.*.fa >My_bacteriaA ...
written 5 weeks ago by shenwei3564.1k
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Comment: C: obtaining a concatenamer of sequences
... It depends on the user. ...
written 5 weeks ago by shenwei3564.1k

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