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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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abundance estimate from cider #493

Closed alhafidzhamdan closed 3 months ago

alhafidzhamdan commented 6 months ago

Hi all, Testing CIDER with my tumour bams, and all went smoothly. Quick question: Which file and what is the column output to use in estimating T-cell abundance in tumour cells? To put it in another way, how do i calculate abundance in this case using your output?

From you readme:

For other tumors, the abundance estimate can be used to estimate immune infiltration and may give insight into diversity, and/or recurrent and cancer specific T-cell clones.

Cheers A

p-priestley commented 6 months ago

You can use either 'minHighQualBaseReads' or 'assignedReads' to determine abundance of each passing sequence.

hongwingl commented 6 months ago

Those are inside the <sampleId>.cider.vdj.tsv.gz file