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Comment: How to access TCGA samples that were treated with a specific drug?
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Qroid
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Thanks. Really appreciate your help with this. This site is such a great resource.
The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
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It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
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Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
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Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
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Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
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Not sure if you wanting to do like this-
cat your_input.bed
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If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
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> Not every read in your data is going to match a guide.
That is also true for sure. Let me clarify what I mean. For every read you should…
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If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
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> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
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Because `dba.analyze` is not meant to be run directly on a peaks file. Have you read the documentation?
In addition, a ChIP-seq experiment…
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> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
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Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/
Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
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No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set.
No idea a…
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