Hello!
I was just wondering if there is a way out to graphically look at the coverage of newly designed primer pairs with QIIME2. For instance, if one wish to compare the taxonomic coverage of two sets of primer pairs to select one out of the two, then a visual output of the coverage results (blasted with Silva nr database, for e.g.) would be useful. My question might seem simplistic to qiime experts. Thanks for your suggestions, if any.
Hi @bsen2018,
We do not have such a tool in QIIME2, but it sounds like you are looking for something like primer prospector.
I hope that helps!
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Thanks @Nicholas_Bokulich, you have rightly understood my question and directed me to a great tool primer prospector!
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Hello @gregcaporaso, my problem is slightly out of QIIME2 and is related to primer prospector. I hope you will help me troubleshoot the error. While I implement the following code:
$ analyze_primers.py -P Primers.txt -f gg_otus_29nov2010/rep_set/gg_97_otus_29nov2010.fasta -v
I get the following error:
Starting 515f
Traceback (most recent call last):
File “/usr/local/bin/analyze_primers.py”, line 168, in
main()
File “/usr/local/bin/analyze_primers.py”, line 163, in main
tp_gap, non_tp_gap)
File “/usr/local/lib/python2.7/dist-packages/primerprospector/analyze_primers.py”, line 947, in analyze_primers
non_tp_mm=non_tp_mm, tp_gap=tp_gap, non_tp_gap=non_tp_gap)
File “/usr/local/lib/python2.7/dist-packages/primerprospector/analyze_primers.py”, line 894, in generate_hits_file_and_histogram
write_primer_histogram(hist_data, graph_filepath)
File “/usr/local/lib/python2.7/dist-packages/primerprospector/analyze_primers.py”, line 233, in write_primer_histogram
’Non 3’ mismatches’, y_axis_size=y_axis_max)
File “/usr/local/lib/python2.7/dist-packages/primerprospector/analyze_primers.py”, line 179, in primer_hit_histogram
yticks(range(0, y_axis_size+2, y_tick_step), size=7)
TypeError: range() integer end argument expected, got numpy.float64.
Please help me in troubleshooting the above error. Thanks in advance!
Hi @bsen2018,
Primer prospector is not really supported on this forum, but @William might have some insight on this issue.
Thanks!
Hi @Nicholas_Bokulich, I got the issue resolved by @William. Sorry to raise the issue on this platform. Thanks!
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