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Recent Replies
Comment: Extract gRNA sequence using cutadapt
by
gernophil
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80
> Can you try lowering the k to k=9?
Wouldn't that mess with the results since all my kmers are 20bp?
> You don't have any duplicate sequ…
Comment: Provean help
by
Mensur Dlakic
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> Else, I will happy to send over the data and kindly perform the analysis for me.
This website is meant to provide advice, not service. I…
Comment: How to access TCGA samples that were treated with a specific drug?
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Qroid
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Thank you! Naive question, but does that list include all treatments in TCGA? I.e. is there anything missing from there, or that's it?
Als…
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dtnondorf
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Interesting! Thank you for such a quick response!
Comment: GATK genomicsDBimport intervals for WGS
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Sd
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I also have similar question. I sliced the genomic bed file with 50kb windows and 1kb padding into ~700 bed files; each bed file contains 9…
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See answer here: https://www.biostars.org/p/9494503/#9494619
Heng Li said: https://twitter.com/lh3lh3/status/1410375781340135424
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Comment: Extract gRNA sequence using cutadapt
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Can you try lowering the `k` to `k=9`?
You don't have any duplicate sequences in your library file? That may be one reason why bbduk is r…
Comment: Extract gRNA sequence using cutadapt
by
gernophil
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This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue.
I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification
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dsull
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Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
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Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
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i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
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> I've also included the txt version of my .csv file
No, you added a screenshot of plain text content, which is counterproductive. You can…
Comment: How to access TCGA samples that were treated with a specific drug?
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At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on.
![drug][1]
For Breast cancer you c…
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Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
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