User: Optimist

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Optimist160
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Posts by Optimist

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Comment: C: Replace fasta Header witha a matching text
... This worked Thanks a ton ...
written 22 hours ago by Optimist160
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Comment: C: Replace fasta Header witha a matching text
... I want to know what command can be used to achieve the purpose. It can be seqkit or anything else ...
written 22 hours ago by Optimist160
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Replace fasta Header witha a matching text
... My fasta header looks like this >name1 ATGCATGCAT My output must look like this >alfaAB --kv file looks like this name1 alfaAB What command can be used to achieve this?? Thank You ...
grep seqkit awk written 22 hours ago by Optimist160 • updated 22 hours ago by GenoMax96k
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Comment: C: Renaming fasta headers according to a matching name list
... I want to replace orf05188 with geneA ...
written 23 hours ago by Optimist160
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Comment: A: Renaming fasta headers according to a matching name list
... Hi Shenwei seqkit replace -k acc2gi.tsv -p "^(.+?) (.+)$" -r "gi|{kv}|ref|\$1| \$2" seqs.fasta > seqs.renamed.fasta Can you modify this command for me? This is my fasta header >orf05188 draft|P. aeruginosa 908|Pseudomonas|orf05188 Scaffold_1 5479915 5478419 len=1497 My output h ...
written 1 day ago by Optimist160 • updated 1 day ago by GenoMax96k
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Combine multiple CARD RGI outputs
... Hi Biostars, I have CARD-RGI outputs (.txt & .json) for multiple genomes. Is there a tool or a python script that can combine these multiple outputs into 1 summary file. Maybe presence absence file or something like that. Thank you ...
rgi card written 29 days ago by Optimist160
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Comment: C: How to extract fasta headers that contains specific text and it's sequence
... Thank you This might not help because most of the 16S rRNA seqs would be conserved (identical). ...
written 4 weeks ago by Optimist160
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Answer: C: How to extract fasta headers that contains specific text and it's sequence
... I have found a solution to this. seqkit rmdup -n -i -j > outfilename Thank you all for the responses Cheers Have a great time!!! ...
written 4 weeks ago by Optimist160 • updated 4 weeks ago by Ram32k
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Comment: C: How to extract fasta headers that contains specific text and it's sequence
... This has worked too. Thank You is there a way to remove duplicate headers along with the associated fasta sequence Looks like most of the genomes have more than 1 16SrRNA sequences (as expected). ...
written 4 weeks ago by Optimist160
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Comment: C: How to extract fasta headers that contains specific text and it's sequence
... filter_fasta.py has worked. ...
written 4 weeks ago by Optimist160

Latest awards to Optimist

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Popular Question 21 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
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Popular Question 3.4 years ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
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