User: gundalav

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gundalav240
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Posts by gundalav

<prev • 46 results • page 1 of 5 • next >
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How to show all columns after performing GenomicRanges::subsetByOverlaps
... 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)), ...
R bioconductor genomicrange gwas written 11 weeks ago by gundalav240 • updated 11 weeks ago by Sean Davis24k
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Comment: C: Can or should we perform feature counting with `bedtools intersect -c`?
... @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 5 months ago by gundalav240
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Can or should we perform feature counting with `bedtools intersect -c`?
... 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 ...
bedtools featurecounts rna-seq written 5 months ago by gundalav240
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Comment: C: How to recover treated/control count from DESeq2 output
... Thanks. `airway@assays$data$counts` is that normalized or not? If not how can I get the normalized one from S4? ...
written 10 months ago by gundalav240
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How to recover treated/control count from DESeq2 output
... 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) #> ...
rna-seq dseq2 written 10 months ago by gundalav240 • updated 10 months ago by b.nota3.6k
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Comment: C: How to calculate RPKM from featureCounts output
... @b.nota i.e. 100 + 30 = 130 (sum of 7th column of featureCounts output)?? ...
written 12 months ago by gundalav240
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Comment: C: How to calculate RPKM from featureCounts output
... @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 12 months ago by gundalav240
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Comment: C: How to calculate RPKM from featureCounts output
... I'm interested in processing from featureCounts not htseq. ...
written 12 months ago by gundalav240
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How to calculate RPKM from featureCounts output
... 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 ...
rna-seq written 12 months ago by gundalav240 • updated 12 months ago by James Ashmore2.3k
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Problem Converting BAM to SAM on to Amazon-S3 Using Samtools
... 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 ...
samtools amazon-web-services amazon-ec2 amazon-s3 written 12 months ago by gundalav240 • updated 12 months ago by Devon Ryan76k

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