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Comment: How to access TCGA samples that were treated with a specific drug?
C: GATK genomicsDBimport intervals for WGS
Comment: DiffBind: no peaks in DBA
Comment: When should I NOT apply batch correction for my single-cell RNAseq data?
Comment: Bacterial plasmid analysis
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
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Comment: Base Quality Score Recalibration with different reference genome
by
dtnondorf
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Interesting! Thank you for such a quick response!
Comment: GATK genomicsDBimport intervals for WGS
by
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…
Comment: Base Quality Score Recalibration with different reference genome
by
GenoMax
142k
See answer here: https://www.biostars.org/p/9494503/#9494619 Heng Li said: https://twitter.com/lh3lh3/status/1410375781340135424 <!-- th…
Comment: DiffBind: no peaks in DBA
by
yvonneh
▴ 10
Ok fixed!
Comment: Extract gRNA sequence using cutadapt
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GenoMax
142k
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
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gernophil
▴ 80
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
by
dsull
★ 5.9k
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…
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
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…
Comment: Split Fastq Files Into Chunks Of 1M Reads
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thomas.heigl.ibk
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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, …
Comment: DiffBind: no peaks in DBA
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Ram
43k
> 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?
by
GenoMax
142k
At the GDC portal you have to turn the "therapeutic agents" toggle under "Clinical Data Analysis" on. ![drug][1] For Breast cancer you c…
Answer: Loss of 'var' using concatenation of AnnData objects
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Hugo
• 0
Similar question has been asked and answered on [scverse discourse](https://discourse.scverse.org/t/loosing-anndata-var-layer-when-using-sc…
Comment: Bacterial plasmid analysis
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Zamin Iqbal
▴ 20
Hi Nicole. 1. The clustering will be quite different between pling and the rep types (because plasmids with one rep type can still be ve…
Comment: Do I need to go back and filter my long-reads?
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Ram
43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx
by
bk11
★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
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