Use this workflow sample to extract unmapped reads from an input SAM/BAM file.
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
The workflow sample "Get Unmapped Reads" can be found in the "NGS" section of the Workflow Designer samples.
The workflow looks as follows:
<center> <br> <img src="/wiki/download/attachments/16123235/Get Unmappet Reads.png"/> <br> </center> |
The wizard has 3 page.
Input SAM/BAM File(s): On this page you need input SAM/BAM file(s).
<center> <br> <img src="/wiki/download/attachments/16123235/Get Unmappet Reads_1.png"/> <br> </center> |
Filtration: On this page you can change the filtration parameters.
<center> <br> <img src="/wiki/download/attachments/16123235/Get Unmappet Reads_2.png"/> <br> </center> |
The following parameters are available:
Accept flag | Only output alignments with the selected items. Select the items in the combobox to configure bit flag. Do not select the items to avoid filtration by this parameter. |
Skip flag | Skip alignment with the selected items. Select the items in the combobox to configure bit flag. Do not select the items to avoid filtration by this parameter. |
Region | Regions to filter. For BAM output only. chr2 to output the whole chr2. chr2:1000 to output regions of chr 2 starting from 1000. chr2:1000-2000 to ouput regions of chr2 between 1000 and 2000 including the end point. To input multiple regions use the space seprator (e.g. chr1 chr2 chr3:1000-2000). |
MAPQ threshold | Minimum MAPQ quality score. |
Results: On this page you need input output parameters.
<center> <br> <img src="/wiki/download/attachments/16123235/Get Unmappet Reads_3.png"/> <br> </center> |