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Space Ranger 1.3.0 has been wrapped in Partek Flow as Space Ranger task. The task takes .fastq and .jpeg/.tiff files as input and performs alignment, filtering, barcode counting, and UMI counting. The output is gene expression count matrix in a .h5 format (both raw and filtered are available for download via Task Details), as well as a .zip file with spatial files (image). Note that the Space Ranger task in Partek Flow does not include all the options and uses cases covered by the Space Ranger pipelines of 10x Genomics.

Note: when use using the Space ranger Ranger task in Partek Flow, there is are more restrictions on the sampe name-- sample name can only contain letters, digits, underscores and dashes. Please Edit the sample names on Data tab in Partek Flow to remove any other characters characters, e.g. space etc.

Running Space Ranger in Partek Flow

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Downloading a reference is a separate task and may take some time. However, the reference will become immediately available in the Cell Ranger 6.0.0. reference drop down dropdown (Figure 4).

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The sample table under Input options has one row per sample (Figure 2). Image file is required, and that is a single hematoxylin and eosin brightfield image in either .jpg or .tiff format. Click on the Browse button under Browse image file and the file browser will come up. Point to the image file and push Continue. The Probe set file is optional; it is a .csv file specifying the probe set used (=target panel).

If you want to specify the sample's slide and area information, tick mark the box by the Use slide serial number file and then click Browse to point to the file. The file should be tab-delimited with samples on rows. The first column is the sample name, the slide name is on the second column, slide area is on the third column.

Click on the Configure link in the Advanced options section to open the Advanced optionsOptions dialog (Figure 5). Use R1 length to hard trim the R1 reads to specified length; use R2 length to hard trim the R2 reads to specified length. Use the Memory limit option to cap the RAM usage (in GB).

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The result of Space Ranger task is the Single cell counts data node, which contains the gene expression data. Double click the Single cell counts node to invoke the report the task report (Figure 6) which is the same as the ‘Summary HTML’ from the original 10x Genomic pipelines. Task report is sample based. You can use the dropdown list in top left to switch samples (not shown in Figure 6).  Each report consists of two pages: Summary and Analysis. For deatailsdetails, please visit 10x Genomics web page.

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