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Hello,
Using a one-week old fresh install of bcbio, I am running into the following error during a bulk RNA-seq run:
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[2021-11-22T13:47Z] Converting Sailfish to Sleuth format.
[2021-11-22T1…
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Overall strategy: sample all reads of cells from a list of cell-ids with known cell-type
- a simple database (e.g. sqlite, even a flat textfile could do it) that stores: cell-id, path to fastqs, ce…
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The submission sheet preparation was done by Annika and Tao
https://docs.google.com/spreadsheets/d/1KxSKLNLf2MueCo-gbw5pVCBfSvGbfOOZ/edit#gid=1176823628
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Hi there,
I'm very interested in this method and managed to get the bMIND() method running using some TCGA bulk RNA-seq data and our own predicted cell type proportions based on our scRNA-seq data.…
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https://mp.weixin.qq.com/s/wayWTZ1wizfoqtbVvQK4Gg
ixxmu updated
2 years ago
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The data needs to be in raw format (unaligned FASTQ files or aligned BAM, with the appropriate GTF/GFF and FASTA references) and generated using poly(dT) primers.
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Hi! I am wondering how did you combine the pseudobulk data and TCGA data before hierarcheal clustering? Since I couldn't find these codes in the repo. Could you direct me to how to normalize the two d…
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All projects are supposed to be sending is parallel bulk RNA-seq data, which we will want to process in parallel to the single cell data. Since we have resolved to using Alevin for the single cell pro…
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https://mp.weixin.qq.com/s/ZCOoeQU6ysK9G8apTnfjvQ
ixxmu updated
2 years ago
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https://mp.weixin.qq.com/s/UcPjSZRzgNXggDLAnnWx5Q
ixxmu updated
2 years ago