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With the sorted, indexed, filtered for uniquely mapped and resolved for spliced alignment reads, HAMR tabulates the total number of high-quality mismatches at each candidate genomic site. HAMR then excludes the possibility that the observed mismatches are not due to sequencing error, SNP or RNA editing.
Input Data:
| Input | Description | Example |
|---|---|---|
| BAM file | BAM file with sorted, indexed, filtered for uniquely mapped and resolved for spliced alignment reads | iplantcollaborative > example_data > HAMR_tutorial -> resolved_splice_alignments |
RUN HAMR
- Click on "Apps" tab in the Discovery Environment and search for 'HAMR'.
- Under Inputs section, provide input BAM file and reference genome. Leave prediction model file as default.
- Provide an output file and output prefix in outputs section or leave it to defaults.
- Under parameters, provide min read quality= 30, min read cov= 10, seq error rate= 0.05, Hypothesis= H4, Max p-val= 0.01, Max FDR= 0.05, Max ref prec= 0.05 or change as desired.
- Under optional parameters, indicate that the data is paired-end (pe) and filter-ends (fe). Filter-ends excludes the first and last positions in the read from the analysis.
Output/Results
| Output | Description | Example |
|---|---|---|
| HAMR | positions predicted to contain modified nucleotides | iplantcollaborative > example_data > HAMR_tutorial -> HAMR_output |
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