User: dieunelderilus

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Posts by dieunelderilus

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... Thanks a lot! Please I would be happy if you can send the nr.$id.fa forme to me at derilus.dieunel@upr.edu or dieunelderilus@gmail.com. But should keep testing to see where I am wrong, because this is a very interesting tools. ...
written 8 weeks ago by dieunelderilus0
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... Thanks they are copied here : wc -l 3041.acc.txt 430402 3041.acc.txt wc -l 3041.taxid.txt 9872 3041.taxid.txt Note that I could not reproduce the tutorial, the option 2 of the step three works but , but could not pass the stp4 (make blasted). You did not provide how to d ...
written 8 weeks ago by dieunelderilus0
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... I need to retrieve get a new database for Chlorophyta with taxid 3041. the perl one-liner script outputs an empty file for watever taxid I use . I could not even reproduce the tutorial. It could be trivial but I don't know why I don't get it. thank you for your assistance DD ...
written 8 weeks ago by dieunelderilus0
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... Sorry, it was a problem in editing the message. the id is 6656 ...
written 8 weeks ago by dieunelderilus0
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... I am getting a problem with taxonkit tutorial. I get stock in the step 3 (option 1). After retrieving FASTA sequences from pre-formated blastdb, the perl one-liner that used to unfold records having mulitple accessions output an empty nr.$id.fa.gz. Please any suggestions ? ...
written 9 weeks ago by dieunelderilus0 • updated 8 weeks ago by shenwei3564.5k
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... I am following to this tutorial to filter the non-redundant database but I get stock in step 3. You suggest to NOT directly download nr.gz from ncbi ftp, in which the FASTA headers are not well formatted. However the link you provide to download the pre-formatted nr database is not working. P ...
written 9 weeks ago by dieunelderilus0
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Comment: C: Filter the non-redundant NCBI database based on taxonomy
... Thanks for sharing the tutorial , I am following the discussion and read the tutorial to see if could filter the the nr based on taxonomy DD ...
written 9 weeks ago by dieunelderilus0
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Filter the non-redundant NCBI database based on taxonomy
... Please is is there any way to extract all the eukaryotic reads from the non-redundant NCBI database ? What would be the exact command line that would help me to do that ? or where can I find the non-redundant Eukaryotic database ? Thanks in advance for your support DD ...
ncbi genebank database written 9 weeks ago by dieunelderilus0 • updated 9 weeks ago by vkkodali960

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