User: medamato

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medamato0
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Posts by medamato

<prev • 10 results • page 1 of 1 • next >
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Comment: C: batch download from ncbi mitochondrial resources
... dear genomax, I have no idea what happened, restarted the computer and the code is working now but only recovers 6 sequences, not 23 (out of the 71 Aves 18S) awk -F '\t' '{if ($0 ~/NC/ && $0 ~/18S/) print $12,$13,$14}' gene_result.txt | xargs -n 3 sh -c 'efetch -db nuccore -id $0 -seq_start ...
written 4 weeks ago by medamato0
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Comment: C: batch download from ncbi mitochondrial resources
... I am using Cygwin I tried to install Ubuntu but something prevented from doing so, windows updates only if we are on campus. We are still on lockdown, working from home. maybe something is missing in Windows updates ? I will consult with the university . thnx a lot for all your help. I will let you ...
written 4 weeks ago by medamato0
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Comment: C: batch download from ncbi mitochondrial resources
... in the line of error that I transcribed there is something very strange, ****+A dmin@NBDLN587A3839.ad.uwc.ac.za'**** uwc.ac.za is the end of my university address , however I logged in ncbi with my gmail personal account. is it possible that this is some kind of issue generated by the university ...
written 4 weeks ago by medamato0
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Comment: C: batch download from ncbi mitochondrial resources
... Thanks genomax I did so, and did not work. In order to prevent typing mistakes I saved the file with your name and tried again. still get the same error messages ...
written 4 weeks ago by medamato0
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Comment: C: batch download from ncbi mitochondrial resources
... thnx genomax. I tried your code followed by how to wrote the fasta: awk -F '\t' '{if ($0 ~/NC/ && $0 ~/18S/) print $12,$13,$14}' gene_result.txt | xargs -n 3 sh -c 'efetch -db genome -id $0 -seq_start $1 -seq_stop $2 -format fasta' > Aves18b.fa I get a very large message starting with ...
written 4 weeks ago by medamato0
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Comment: A: batch download from ncbi mitochondrial resources
... I have a related query, I am trying now to extract nuclear genes. e.g. in genes I am searched using the terms: (18S ribosomal RNA) AND Aves I recover a list of 71 entries. I use a similar code as above awk -F '\t' '{if ($12 ~/NC/ && $8 ~/(18S ribosomal RNA)/) print $12,$13,$14}' info18 ...
written 4 weeks ago by medamato0
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Comment: C: batch download from ncbi mitochondrial resources
... Dear genomax, thanks for your reply. I run the script and only gets a list of this sort in the screen: NC_011124.1 1103 2677 NC_035814.1 1102 2669 NC_008417.1 1101 2677 NC_008420.1 1102 2679 ..etc .. but i need a fasta file like the one that worked for felidae. I appreciate your help. best regard ...
written 5 weeks ago by medamato0
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Comment: C: batch download from ncbi mitochondrial resources
... Dear genomax I am asking for help again, I tried my self but my understanding of the scrip is not too good and could not find a solution in the entrez programming manual . I have to keep analyzing different taxa and different genes, what terms of the code do I need to modify for this ? (sorry don't ...
written 5 weeks ago by medamato0
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Comment: A: batch download from ncbi mitochondrial resources
... thank you genomax! it worked. slowly, got there. :) ...
written 5 weeks ago by medamato0
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batch download from ncbi mitochondrial resources
... Dear group, I am relatively new to these resources. I would like to download a batch of sequences from the mitochondrial reference sequences in ncbi. For instance. would like to get all 16S rRNA sequences from Felidae (https://www.ncbi.nlm.nih.gov/genome/browse#!/organelles/Felidae) in fasta format ...
gene sequence alignment written 6 weeks ago by medamato0

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