Chen Ying comments

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                                            Chen Ying

Large numebr of BAM files leads to Error in `vec_interleave_indices()`:

Hi @NikoLichi , Thanks for getting back so quickly, and I am happy that the mergedAnno step runs through. For the warning you see in the mergedAnno step warning is...

Large numebr of BAM files leads to Error in `vec_interleave_indices()`:

Hello @bernardo-heberle , Thanks for reaching out, and sorry for the late reply. I understand your concern about whether the results might be affected, but I can assure you that...

Large numebr of BAM files leads to Error in `vec_interleave_indices()`:

Hi @bernardo-heberle , I'm glad the previous error has been resolved, and I appreciate your detailed description of the context—it really helps me understand the situation. The current error is...

Large numebr of BAM files leads to Error in `vec_interleave_indices()`:

Hi @bernardo-heberle , Thanks for the updates. It looks like the memory issue is due to an R out of memory error, which may be caused by the use of...

Are there tissue samples available?

Hi @jackwgoodall , thank you for using SG-NEx data resource and for pointing out that the description is unclear. For the core datasets, we have generated 7 core cell lines,...

question about sequin concentration

Hi @sparthib, We are glad to know that you find this resource helpful! And I am very sorry for getting back lately. For the spike-in concentration, 1% means that of...

Transcripts identified by Bambu have a CPM or count value of 0 in all samples

Hi @alexyfyf Thanks for using Bambu and spotting this issue. We did observe 0 count estimates for novel transcripts. There are two scenarios that this might happen: 1) the novel...

Error in xgb.get.handle(object): 'xgb.Booster' object is corrupted or is from an incompatible xgboost version.

Hi @nick-youngblut , thanks for reporting this. However, I believe there must be some confusion here. As you know, xgboost can refer to both the software or the R package....

BiocParallel error when using Bambu in quantification mode

Hi @apsteinberg , Sorry for the late reply! Based on the error message, it looks like a few samples had zero reads aligned to the reference genome. This could be...