abundance estimate from cider

[alhafidzhamdan]

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]

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

[hongwingl]

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