User: gundalav
gundalav • 260
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Posts by gundalav
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... I have the following code:
library(Gviz)
library(Mus.musculus)
library(data.table)
library(OrganismDbi)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
# Define bam file -----
adipose_bam <- "myfile.bam"
...
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... Yes I have. BTW what I mean by RG tag is the one indicated in every read not as `@RG` header. ...
written 12 months ago by
gundalav • 260
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... I have a BAM file that looks like this:
![enter image description here][1]
As you notice that the barcodes are included as part of read names.
Then I'm trying to use a [tool called chromVAR][2] that require `RG` tag to be included in the BAM file. RG tags are used to distinguish reads from diffe ...
written 12 months ago by
gundalav • 260
• updated
11 months ago by
finswimmer ♦ 11k
1
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... I have the following two [GenomicRanges][1] objects. First one `gr1` is this:
library(GenomicRanges)
set.seed(1)
gr1 <- GRanges(
seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges=IRanges(1:10, width=10:1, names=head(letters,10)),
...
written 17 months ago by
gundalav • 260
• updated
17 months ago by
Sean Davis ♦ 25k
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... @ATPoint Thanks for your reply. Speed is less of a concern at the moment, but rather the **correctness** of Method1. I tried using `cut -f1,2,6,7,8,9`. But the Method1 is totally uncorrelated (different) from Method2 and Method3. I need to be convinced why Method1 is incorrect. Your enlightenment wi ...
written 20 months ago by
gundalav • 260
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1
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5 follow
1
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... I have the following BAM file and a annotation file.
The BAM is a paired end alignment.
What I want to do is to calculate reads (as fragment) count in
I can do it with the following three methods.
- **Method1:** [bedtools intersect][1]
- **Method2:** [bedtools multicov][2]
- **Method3:** [fea ...
written 20 months ago by
gundalav • 260
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... Thanks. `airway@assays$data$counts` is that normalized or not? If not how can I get the normalized one from S4? ...
written 2.1 years ago by
gundalav • 260
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10 follow
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... I have the following DESeq2 code and the corresponding results
suppressMessages(library(DESeq2))
suppressMessages(library(airway))
data(airway)
airway_se <- airway
airway_dds <- DESeqDataSet(airway_se, design = ~cell + dex)
deseq <- DESeq(airway_dds)
#> ...
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... @b.nota i.e. 100 + 30 = 130 (sum of 7th column of featureCounts output)?? ...
written 2.2 years ago by
gundalav • 260
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... @b.nota in other words the `totalReads` in the calculation *is not the total assigned reads to the genes*? So I have to directly count from the BAM file? Would prefer to recode cause later need to calculate TPM as well. ...
written 2.2 years ago by
gundalav • 260
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