User: weissert

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weissert0
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Posts by weissert

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Comment: C: Adapt perl script
... a) Reformat the header of the fasta sequences to be: >tRNA_name predicted_anti-codon_positions b) Remove predicted introns c) add CCA to the sequence tail does it help`? ...
written 3.5 years ago by weissert0
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Comment: C: Adapt perl script
... perl is not a must :-) I copied your script and saved it in script.sed Running on Ubuntu, executed the following commmand: sed script.sed codonpos.txt This is what happend: sed: -e expression #1, char 10: unterminated `s' command ...
written 3.5 years ago by weissert0
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Comment: C: Adapt perl script
... true. But the script is the only thing on hand and it requires the input of both file 1 and file 2. ...
written 3.5 years ago by weissert0
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Adapt perl script
... I am not a Perl coder and hope to find help in this forum. I aim to run the script.pl, shown below on the following input but do not get the desired output: here is my desired output: >Pseudo_TTA 33-35 AGATCTGTAAGCTCAAAATGGTAGAGCTCTCGTTATGAGAGTTTGGTGGTTCGAATCCACCCAGATCTGcca >His_ ...
software error gene sequence written 3.5 years ago by weissert0 • updated 3.5 years ago by lakhujanivijay4.6k
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Comment: C: Reformat fasta header
... To clarify my question. I have two files one is in fasta format the other one is the cove output of tRNAscanSE, indicating the secodnary structure of my tRNA and the position of the Anticodon. I want my header like this: >Sup_TTA(Anticodon) 33-35(Anticodon positiion) >His_GTG 34-36 ...
written 3.5 years ago by weissert0
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Reformat fasta header
... Hi, I have trouble to reformat my current fasta file header. This is the header it need to be like: >tRNA_name predicted_anti-codon_positions This is my current header: >chrA01_622419_622487_+_Sup_TTA_28.44 >chrA01_2528533_2528604_+_His_GTG_63.70 This is the fileformat I co ...
gene sequence written 3.5 years ago by weissert0
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Run old tRNAscanSE output on tDRmapper
... Hi erverybody, I am trying to get tDRmapper running on an tRNAscanSE output version 1.3.1 [https://github.com/sararselitsky/tDRmapper][1] Unfortunately the script provided only takes input from gtRNAdb which is the output of tRNAscanSE 2.0 The source code of 2.0 is not public yet. Here is the link ...
sequence alignment rna-seq written 3.5 years ago by weissert0

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