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broadinstitute / Drop-seq

Java tools for analyzing Drop-seq data
MIT License
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about the detectbeadsubstitutionerrors module! #304

Open 10KGenomics opened 2 years ago

10KGenomics commented 2 years ago

Dear sir

Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows: image

What the Intended_ size、neighbor_size mean? Is this the number of overwritten reads of the cell barcode? If the repaired column is true, correct the barcode base and enter the next analysis.

jamesnemesh commented 2 years ago

Hi,

The intended size is the number of UMIs for what we believe is the original error free cell barcode. The the neighbor size is the number of UMIs in a related cell barcode that we think should be merged. Repaired=T means that the two sets of UMIs will be merged into the intended barcode.

Your barcodes look very different from the standard dropseq or 10x reaction - it looks like you have a cell barcode, UMI, and polyA tail on every barcode. Are you running a very different protocol and you’re confident in retaining all of those bases?

-Jim

On May 4, 2022, at 5:06 AM, caijingtao1993 @.***> wrote:

Dear sir

Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows: https://user-images.githubusercontent.com/67781404/166652335-22bd1dfd-d5dc-484e-bfc4-4f899a6b752b.png What the Intended_ size、neighbor_size mean? Is this the number of overwritten reads of the cell barcode? If the repaired column is true, correct the barcode base and enter the next analysis.

— Reply to this email directly, view it on GitHub https://github.com/broadinstitute/Drop-seq/issues/304, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCZXJ2EAK6U5G52SPTYPKDVII423ANCNFSM5VBKCO7Q. You are receiving this because you are subscribed to this thread.

10KGenomics commented 2 years ago

Hi, The intended size is the number of UMIs for what we believe is the original error free cell barcode. The the neighbor size is the number of UMIs in a related cell barcode that we think should be merged. Repaired=T means that the two sets of UMIs will be merged into the intended barcode. Your barcodes look very different from the standard dropseq or 10x reaction - it looks like you have a cell barcode, UMI, and polyA tail on every barcode. Are you running a very different protocol and you’re confident in retaining all of those bases? … -Jim On May 4, 2022, at 5:06 AM, caijingtao1993 @.***> wrote: Dear sir Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows: https://user-images.githubusercontent.com/67781404/166652335-22bd1dfd-d5dc-484e-bfc4-4f899a6b752b.png What the Intended_ size、neighbor_size mean? Is this the number of overwritten reads of the cell barcode? If the repaired column is true, correct the barcode base and enter the next analysis. — Reply to this email directly, view it on GitHub <#304>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCZXJ2EAK6U5G52SPTYPKDVII423ANCNFSM5VBKCO7Q. You are receiving this because you are subscribed to this thread.

yes. Thank you for your reply, sir. I default both the link sequence and the ployT sequence as part of the barcode, so the barcode is long. What is the basis for determining repaired = t? In addition, EDIT_DISTANCE parameter defaults to 1. If it is set to 2, does it mean that there are two different bases in the barcode sequence and will it be corrected?