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Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
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small test data #97

Closed wangjiawen2013 closed 4 years ago

wangjiawen2013 commented 4 years ago

Dear, This is my first time to use TraCer. In the tutorial, it is said that TraCeR comes with a small dataset in test_data/ (containing only TCRA or TCRB reads for a single cell), while "There should be three cells, each with one productive alpha, one productive beta, one non-productive alpha and one non-productive beta. Cells 1 and 2 should be in a clonotype." So I am perplexed why three cells are generated with only a single cell. Besides, the results showed that some non-TCR genes were expressed according to the Kallisto output, which was inconsistent with the description "containing only TCRA or TCRB reads for a single cell". I wanna know how to explain it.

mstubb commented 4 years ago

There is a test dataset containing sequencing reads from a single cell (cell1). This is used to test the assemble stage.

The test_data directory also contains precomputed TraCeR output from two other cells (cell2 and cell3). This is used in conjunction with the test assemblies to test the summarise stage.

So, three cells in total.

The precomputed data was generated from sequencing reads from the whole transcriptome of those cells and so the Kallisto outputs contain quantifications for other transcripts. I expect Kallisto is able to pseudo-align reads from the cell1 data to some other transcripts and so will report quantifications for these. Given that this is a completely synthetic situation, you should ignore the Kallisto output for the test data.