Getting representative sequences

[Jeyamalar Jeyanathan]

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]

I want to have all the representative sequences of the genus Prevotella. I used Qiime 1 and open reference OTU picking.

[TonyWalters]

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]

Dear Tony,

Thank you. I got all the sequences.

Best regards,

Malar

[mallamu...@gmail.com]

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