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Comment: Extract gRNA sequence using cutadapt
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GenoMax
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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 …
Comment: Extract gRNA sequence using cutadapt
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gernophil
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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…
Answer: VG : No reference-sense paths available in the graph; falling back to generic pa
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anovak
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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…
Comment: Extract gRNA sequence using cutadapt
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gernophil
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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/
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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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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 you …
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> Can you try lowering the k to k=9?
Wouldn't that mess with the results since all my kmers are 20bp?
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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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Interesting! Thank you for such a quick response!
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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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