User: Angie11

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Angie110
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Posts by Angie11

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Removing white space from the beginning of the second field (sequence) in a fasta file
... Hello, Does anyone know of a command (in the linux command line) such as sed to remove white spaces from a specific field only? In my case, I have 2 tab-seperated fields in the format shown below and I would like to remove the white space from the beginning of the second field (the beginning of t ...
fasta sequence protein linux written 15 months ago by Angie110 • updated 15 months ago by Chris Miller21k
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Comment: C: Convert large text file back into a FASTA file
... I see, thank you. I was wondering if there is a command in Linux to reformat a file that is in the messy format above into 2 lines like RamRS did? - Essentially do what the 10101 button does but through the command line, on a large txt file ...
written 15 months ago by Angie110
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Comment: C: Convert large text file back into a FASTA file
... @RamRS, What command did you use to reformat this? Thank you! ...
written 15 months ago by Angie110
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Comment: C: Convert large text file back into a FASTA file
... It seems to be working! Thank you so much Pierre :) ...
written 16 months ago by Angie110
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Comment: C: Convert large text file back into a FASTA file
... Formatted by @RamRS: ``` Bacteroides genus root|cellular organisms|Bacteria|Bacteroidetes/Chlorobi group|Bacteroidetes|Bacteroidia|Bacteroidales|Bacteroidaceae|Bacteroides no rank|no rank|superkingdom|superphylum|phylum|class|order|family|genus10_GL0085768 [gene] locus=scaffold30815_5:6223:7791:- [ ...
written 16 months ago by Angie110 • updated 16 months ago by _r_am31k
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Convert large text file back into a FASTA file
... Hello, Does anyone know of a tool to convert a large .txt file (~850MB) into a .FASTA file? I converted a FASTA sequence file into a txt file using the fasta_formatter of the FASTX tool on Linux so I could combine the accession numbers with descriptions from another txt file using a join command. ...
sequence written 16 months ago by Angie110 • updated 16 months ago by Pierre Lindenbaum131k

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