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bvaldebenitom / SoloTE

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Test Data #5

Closed A1aNNN closed 1 year ago

A1aNNN commented 1 year ago

Hi there,

I've been trying to run the SoloTE script on a BED file and a BAM file that I received from STAR with the parameters --winAnchorMultimapNmax 100, --outFilterMultimapNmax 100, and --outSAMmultNmax 1, but received an error that it's unable to print(samtags_from_star[0]).

Just wondering if you had any test data that I could use to run SoloTE on, and whether the expected outputs for SoloTE are the files barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.

Thanks,

Alan Wang

Screen Shot 2022-11-08 at 2 50 44 PM
bvaldebenitom commented 1 year ago

Hi Alan,

if you are using STAR for single cell RNA-Seq analysis, you should also include the outSAMattributes options to include the CB, UB, CR and UR tags for each alignment, as indicated in the STAR solo documentation.

We will add a sample BAM file to test the pipeline.

If there is anything else, please reach out.

A1aNNN commented 1 year ago

Thanks for your help! Greatly appreciate your time