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HAMR requires that reads map unambiguously to a reference sequence, in order to avoid false-positive mismatches. Workflow-extractUniqueReads, retains uniquely mapping reads and converts to the sorted BAM format. Next step resolving spliced alignments using GATK requires assigning reads in a file to a read-group. Picard AddorReplaceGroups DE app will be used for assignment of read-group.
Input Data:
| Input | Description | Example |
|---|---|---|
| HISAT2 output file | Alignment file in BAM format | iplantcollaborative > example_data > HAMR_tutorial -> mapped_reads |
RUN Workflow-extractUniqueReads
- Click on "Apps" tab in the Discovery Environment and search for "Workflow-extractUniqueReads".
- Click on the app icon and change the name of the analysis and output folder as desired.
- Under Step1- Samtools 1.11 BAM to SAM provide input BAM file from the data store. Example data for this step is provided at iplantcollaborative > example_data > HAMR_tutorial -> mapped_reads -> SRR7947123_1M_1.sorted.bam. In the next step, getuniquereads provide the output file name and click Launch Analysis.
RUN Picard AddorReplaceReadGroups
- Search for the app "Picard" in Apps search window.
- Click on the app icon 'Picard AddorReplaceReadGroups v2.5'.
- Under the Inputs section provide the output from the Workflow-extractUniqueReads. Example data is provided at iplantcollaborative > example_data > HAMR_tutorial -> unique_mapping_reads -> output_sorted.bam. Provide Read group ID, library, platform, platform unit and sample name.
- Under output section, provide the output file name and click Launch Analysis.
Output/Results
| Output | Description | Example |
|---|---|---|
| Assigned read groups | BAM file with assigned read groups | iplantcollaborative > example_data > HAMR_tutorial -> unique_mapping_reads_assignRG -> output.RG.bam |
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