User: gundalav
gundalav • 240
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Posts by gundalav
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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 4 months ago by
gundalav • 240
• updated
4 months ago by
Sean Davis ♦ 24k
0
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1
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396
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1
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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 7 months ago by
gundalav • 240
3
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1
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396
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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 7 months ago by
gundalav • 240
0
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2
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681
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2
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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 12 months ago by
gundalav • 240
6
votes
2
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681
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6 follow
2
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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)
#> ...
0
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... @b.nota i.e. 100 + 30 = 130 (sum of 7th column of featureCounts output)?? ...
written 14 months ago by
gundalav • 240
0
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3
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1.6k
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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 14 months ago by
gundalav • 240
0
votes
3
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1.6k
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3
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... I'm interested in processing from featureCounts not htseq. ...
written 14 months ago by
gundalav • 240
4
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3
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... Lets say the [featureCounts][1] output is this (for convenience only contain 2 genes:
Geneid Chr Start End Strand Length myfile.bam
Xkr4 chr1;chr1;chr1 3214482;3421702;3670552 3216968;3421901;3671498 -;-;- 3634 100
Npbwr1 chr1 5913707 5917398 - 3692 30 ...
written 14 months ago by
gundalav • 240
• updated
14 months ago by
James Ashmore • 2.3k
2
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1
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384
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1
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... In my Amazon EC2 instance I have the following:
ubuntu@ip-333-31-16-230:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 79G 0 79G 0% /dev
tmpfs 16G 8.8M 16G 1% /run
/dev/xvda1 985G 136G 809G 15% /
tmpfs ...
written 14 months ago by
gundalav • 240
• updated
14 months ago by
Devon Ryan ♦ 78k
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