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Update readme in scripts folder
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mourisl committed Nov 23, 2022
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Expand Up @@ -10,10 +10,10 @@ Compute the clonotype diversity in a sample
#### trust-cluster.py
Cluster similar CDR3s based on the trust_cdr3.out or trust_report.tsv file.

#### barcode-filter.py
#### barcoderep-filter.py
Filter the lowly expressed clonotype if it is identical to another highly expressed clonotype in another cell. This strategy is inspired by 10x VDJ pipeline to remove contaminations from diffused mRNAs: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/algorithms/cell-calling.

#### barcode-expand.py
#### barcoderep-expand.py
Put the secondary chains in the barcode_report.tsv file in its own barcode line. This function is useful if a barcode contains multiple cells. trust-airr.pl script can then be used to create AIRR entries for the secondary chains.

#### trust-barcoderep-to-10X.pl
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