How to know if all your sequences have been analyzed
The Analysis Progress chart is a very useful representation, which shows the step of the analysis in which the sequences in your dataset are found.
They can be in different states, each represented by a color:
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- Total: grey
- Without Analysis: white
- With IPS: purple
- With Blast Hits: orange
- Without Blast Hits: red
As an example of the utility of the Progress chart, the analysis progress may allow you to detect that not all your sequences have been analyzed at a specific step in the analysis due to any kind of problem. In the current entry, you will learn how to detect the problem and solve it.
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The Analysis Progress can be represented in the “Charts” menu, by selecting the “Project” statistics.
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A progress chart as the one bellow may reveal that there are some sequences that have not been analyzed with IPS.
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Once this is detected, you can select those which haven’t been analyzed and run IPS again.To do it, you may select sequences by colour, following the same colour code than the above-mentioned for the analysis progress.
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In the specific example of not having all the sequences analyzed with IPS, you should first generate a copy of your project and remove the blast results (“Blast” menu-“Remove Blast”) to be able to see the sequences with IPS (purple) and those without analysis (white), which you can select. If you follow the normal workflow and first make the IPS analysis and then run Blast, sequences will turn orange (with blast hit) or red (blasted with no hits) enabling the possibility to know whether your sequences have been analyzed with IPS or not, as you will not see any more purple sequences.
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Once you have the sequences without analysis selected in the project you have generated, if you want to identify and select those sequences without analysis in your original project, you can use ID lists. ID lists are very simple to generate and can be very useful.
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Now you have the sequences that are not analyzed selected. Run IPS again and confirm, with the Analysis Progress chart that indeed all the sequences have been analyzed.
