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Recent Replies
Comment: Filter snRNA-seq .fastq files based on barcodes
by
GenoMax
150k
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…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
connorjfausto
▴
30
> What is the intent behind doing this?
From our original snRNA-seq Seurat object, we have a small subset (~5% of nuclei) that collaborato…
Comment: Batch correction RNA-seq analysis
by
GenoMax
150k
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
by
ka132
•
0
Unfortunately, I just found out the libraries were prepped separately as well. Thanks for the advice!
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
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
by
jared.andrews07
★
18k
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
by
ka132
•
0
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
by
GenoMax
150k
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
by
ka132
•
0
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…
Comment: Batch correction RNA-seq analysis
by
ka132
•
0
Just sequencing, no common control unfortunately.
Comment: Batch correction RNA-seq analysis
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GenoMax
150k
> samples were **run**
It would help if you clarify "run" part further. What exact part of the experiment was done in two batches. Full …
Comment: Wolfram tech for bio data analysis
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GenoMax
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> Part of the motivation for this is that many universities have a full site-wide license for our software
Is there a publicly available l…
Answer: Batch correction RNA-seq analysis
by
jared.andrews07
★
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If you have no overlap between batches, there are unfortunately no real options. The experiment is confounded. Consider this an expensive a…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
GenoMax
150k
`filterbyname.sh` only works based on information that is found in the **fastq header**. As you can see the barcodes you have are not in th…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
GenoMax
150k
> How would I use the filtered bam files to get the fastq?
If you have the BAM files you can simply use `samtools fastq your.bam` with app…
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