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Recent Replies
Answer: Batch correction RNA-seq analysis
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Just to emphasize, **running on the same kind of instrument at different times does not cause a batch effect**.
But doing RNA preps on…
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BBMap is actively maintained but what you have is an edge case. You can try writing to Brian Bushnell (his email can be found in software i…
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Get the basic gene annotation from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/GRCh37_mapping/gencode.v47lift37.ba…
Comment: bbduk.sh trimming to BAM output file
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Hi,
I appreciate the confirmation -- I worry that I mess up.
Anyway, the input uBAM file has a tag with the barcode+umi sequences req…
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This appears to be a commercially available array. You could contact Arraystar and see if they would be willing to share the annotations: h…
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Using a uBAM input and writing uBAM output is indeed not working directly. Probably because it is an edge case that @Brian likely did not t…
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Use the 10x's BAM splitting tool (https://github.com/10XGenomics/subset-bam ). You should share those BAM's (instead of fastq) since they h…
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> What is the intent behind doing this?
From our original snRNA-seq Seurat object, we have a small subset (~5% of nuclei) that collaborato…
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Since you are stuck with what you have keep this is as another variable (hopefully it is same as two sequencer batches). Generally people (…
Comment: Batch correction RNA-seq analysis
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Unfortunately, I just found out the libraries were prepped separately as well. Thanks for the advice!
Comment: Batch correction RNA-seq analysis
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ka132
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Well, dangit - I just heard back and the same sequencer was used but library prep was done separately. Bummer. Thanks for the assistance.
Comment: Batch correction RNA-seq analysis
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Batch correction as you mention shouldn't even run, I expect ComBat-seq will yell at you about confounded covariates if you try.
But as me…
Comment: Batch correction RNA-seq analysis
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ka132
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The actual experiment and collection of samples were done at same time. Library prep was definitely done by same person using same protocol…
Comment: Batch correction RNA-seq analysis
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There should be no appreciable batch effect because of sequencing, as long as following is true. The same sequencer (or at least type i.e. …
Comment: Batch correction RNA-seq analysis
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ka132
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yeah.... this is what I was afraid of. I wish this was a lesson that I needed to learn, but again I had no input on the processing up to th…
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