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Recent Replies
Comment: Differing number of reads for read 1 and 2 in fastq's from a subset bam file
by
michael
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0
Hi Pierre, thanks for the suggestion. I've just tried it again with `-F 2304` and unfortunately I'm getting the same issue: 30205 for my fi…
Comment: Overlapping regions in a BED file
by
Matej
•
0
Maybe answer doesn't have to be specific to this file, what is a simple explanation why would two lines in BED file have the same coordinat…
Comment: Overlapping regions in a BED file
by
Matej
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I'm not sure, I downloaded the bed file from [here][1]. I also found it weird that it had this extra column but I didn't know what to make …
Comment: Overlapping regions in a BED file
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what's the meaning of the columns 'mRNA' and 'gen' ?
Comment: Bulk RNA-seq time course data with unknown sample sizes?
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HI @atpoint . Thanks for the feedback. I have 13 time points; sampled every 4 hours over a 14 hour time period. I have some additional data…
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1 5262 5712 E4287_5.mRNA1 449 + . . . 1 450 0 mRNA
1 5262 5712 E4287_5 449 + …
Comment: Bulk RNA-seq time course data with unknown sample sizes?
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You have one pool of RNA, that makes it n=1. The readout is the average over the sacrified population. I see no way to come up with a credi…
Answer: What does it mean by "dynamics"?
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Dunois
★
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Sounds like a homework question to me.
Did you try and read the abstract? The meaning of dynamics is quite readily apparent. I've bolded…
Comment: Overlapping regions in a BED file
by
Matej
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I've edited my question with couple of examples. In the examples provided, the regions don't just overlap, they are exactly the same and I'…
Comment: Overlapping regions in a BED file
by
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multiple transcripts, interleaved genes: the question is why wouldn't they overlap ? please, show us and example.
Comment: Overlapping regions in a BED file
by
Matej
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Okay yeah, maybe I wasn't focused enough in my question, my main question is how can coding regions overlap in a BED file
Comment: Overlapping regions in a BED file
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There are many (unrelated) questions here without context (what is "separate tracks for annotation" ? "how can coding regions overlap in a …
Answer: How to make a TSS enrichment plot in ATAC-seq analysis?
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Trivas
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Not sure what the Score is actually quantifying, but you can do a simple min-max normalization to force the score values to be between 0 an…
Comment: Counting all samples numbers for every gene
by
rpolicastro
8.9k
Tidyverse solution.
```
library("dplyr")
df |>
group_by(Gene) |>
summarize(across(!Variant, sum), .groups="drop")
```
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