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Please clarify the specification for input to Lariat #19

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zamaudio opened this issue Dec 14, 2018 · 0 comments
Open

Please clarify the specification for input to Lariat #19

zamaudio opened this issue Dec 14, 2018 · 0 comments
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@zamaudio
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zamaudio commented Dec 14, 2018

In the .fasth files being input to lariat, I noticed that there are 3 variations on the 10X barcode field

The readme says:

The 10X barcode string is of the form ACGTACGTACGTAC-1

I found that barcodes not in the whitelist appear as AGCTAGCTAGCTAGCT

Barcodes that are in the whitelist and found in the fastq seem to be marked as

AGCTAGCTAGCTAGCT-1,AGCTAGCTAGCTAGCT

Barcodes that mismatch by one base at the beginning of the barcode seem to be considered still as a match and seem to be specified by:

AGCTAGCTAGCTAGCT-1,GGCTAGCTAGCTAGCT

where the barcode at the beginning is the actual barcode it maps to and the one after the -1, is the barcode read from the fastq that mismatches by one base only at the beginning.

Can someone please confirm this specification?

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