Getting representative sequences

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Jeyamalar Jeyanathan

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May 26, 2020, 8:40:57 AM5/26/20
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I want to have the representative sequences (fasta) belong to one genus. Can anyone help me how I can get this in Qiime 1. The out picking method I used was open reference. 

Thank you

Jeyamalar Jeyanathan

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May 26, 2020, 8:44:03 AM5/26/20
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I want to have all the representative sequences of the genus Prevotella. I used Qiime 1 and open reference OTU picking.

TonyWalters

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May 26, 2020, 9:37:03 AM5/26/20
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Hello,

There should be an taxonomic assignments file, that matches the representative sequence identifier to the taxonomy strings. (I think it will be in the uclust_assigned_taxonomy).

If you can find this file, maybe you can do a grep command like this:
grep "Prevotella" X > prevotella_ids.txt
where X is the taxonomic assignments file.

Then the desired IDs should be in the prevotella_ids.txt file.

Next filter the rep_set.fna file with the http://qiime.org/scripts/filter_fasta.html script and pass the prevotella_ids.txt file as the --seq_id_fp parameter.

-Tony

jemaj...@gmail.com

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Aug 19, 2020, 3:35:28 PM8/19/20
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Dear Tony,
Thank you. I got all the sequences.

Best regards,

Malar

mallamu...@gmail.com

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Nov 24, 2020, 11:06:21 AM11/24/20
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Hello sir
Hope you are fine and doing good.
Please have a look at my error while running the command validate_mapping_file.py
As I am getting an unwanted error
Traceback (most recent call last):
  File "/usr/local/bin/validate_mapping_file.py", line 162, in <module>
    main()
  File "/usr/local/bin/validate_mapping_file.py", line 158, in main
    disable_primer_check, added_demultiplex_field, suppress_html)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 97, in check_mapping_file
    added_demultiplex_field, strip_quotes=False, suppress_stripping=True)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 182, in process_id_map
    added_demultiplex_field)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 822, in check_header
    desc_ix, bc_ix, linker_primer_ix, added_demultiplex_field)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 888, in check_header_required_fields
    if (header[curr_check] != header_checks[curr_check] and
IndexError: list index out of range
Please help me out

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