Analyzing ambiguous alignments #267
kclem
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Troubleshooting
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If you have an unexpected number of ambiguous alignments, you can figure out what is going on using these strategies:
Use a script to analyze ambiguous alignments here. You can download and run it (
python plotAmbiguous.py
) on a completed CRISPResso run (run with the '--write_detailed_allele_table' parameter).Here are the parameters:
The script will pull out ambiguous reads and plot allele tables showing the alignment to the relevant amplicons.
You can also use these flags to visualize ambiguous reads by adding them to both references or the first reference:
--expand_ambiguous_alignments
If more than one reference amplicon is given, reads that align to multiple reference amplicons will count equally toward each amplicon. Default behavior is to exclude ambiguous alignments. (default: False)
--assign_ambiguous_alignments_to_first_reference
If more than one reference amplicon is given, ambiguous reads that align with the same score to multiple amplicons will be assigned to the first amplicon. Default behavior is to exclude ambiguous alignments. (default: False)
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