User: nmkn

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nmkn0
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Posts by nmkn

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Remove Fasta Sequences with Duplicate IDs (but with different Descriptions) & Ap
... Any suggestions to work this as a loop for hundreds of files? ...
written 10 months ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... This seqkit worked and was easy! If you add it as an answer I can marked as "accept" ...
written 14 months ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... Thanks for the explanation. I can get the awk step to work using only one fasta file, but when I concat two files and use as input it doesn't work: awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' |\ < sample_file > sample_linear.out ...
written 14 months ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... Just to clarify the steps: 1. (cat) I concatenate all hundreds of my fasta files into ONE fasta file? 2. (awk) this is the linearize step How are the next two steps working? I tried providing the input file but it errors: sort -t $'\t' -k1,1 -u |\ < fasta.file_linearize.out ...
written 14 months ago by nmkn0
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Comment: C: Remove extra sequences without unique names from fasta
... The short answer is it doesn't matter which one I keep. ...
written 14 months ago by nmkn0
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Remove extra sequences without unique names from fasta
... I have hundreds of large fasta files (with almost hundred sequences in each). In some files, I have duplicate sequence NAMES but the sequence itself is NOT a duplicate. I have found other similar posts, but they want to remove duplicate sequences: https://www.biostars.org/p/3003/, https://www.bios ...
fasta duplicates sequence uniq bash written 14 months ago by nmkn0 • updated 14 months ago by Pierre Lindenbaum122k
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Comment: C: how to convert a long fasta-file into many separate single fasta sequences
... How could this be modified to: 1. Instead name the output file(s) the same as the input file and perhaps appended with the corresponding sequence name? 2. Run as a loop so that this could be used to split hundreds of different input files (each with different names corresponding to gene names). ...
written 16 months ago by nmkn0
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Comment: C: randomly sample sequences of fasta file per sample name
... That solves it and it was very fast - thank you very much! And thank you everyone else for your answers too. ...
written 16 months ago by nmkn0
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Comment: C: randomly sample sequences of fasta file per sample name
... Thank you very much! This perl option works well and I think will be the most efficient for many files. Just a follow up - how can I get this to work as a loop since I have hundreds of fasta files? Sorry if that wasn't clear in the original post. I'm having issues: for file in *.fasta; do (perl ...
written 16 months ago by nmkn0
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Comment: C: randomly sample sequences of fasta file per sample name
... Thank you, but I'm not sure if this does what I want. First, I have standard fasta files not .tsv files. Also, how does this randomly select one sequence per sample name and paste into a new file? I apologize if i just don’t understand. ...
written 16 months ago by nmkn0

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