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User: gundalav

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gundalav • 240
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Posts by gundalav

<prev • 49 results • page 1 of 5 • next >
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How to remove the squished track in Give AlignmentTrack()
... 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" ...
rna-seq written 16 days ago by gundalav • 240
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Comment: C: How to add RG tags in a single cell BAM file where each group indicate barcode
... Yes I have. BTW what I mean by RG tag is the one indicated in every read not as `@RG` header. ...
written 4 weeks ago by gundalav • 240
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How to add RG tag into the optional field in a BAM file
... 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 ...
single-cell bam samtools sequencing written 4 weeks ago by gundalav • 240 • updated 15 days ago by finswimmer ♦ 2.8k
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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 6 months ago by gundalav • 240 • updated 6 months ago by Sean Davis ♦ 24k
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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 9 months ago by gundalav • 240
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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 9 months ago by gundalav • 240
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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 14 months ago by gundalav • 240
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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 14 months ago by gundalav • 240 • updated 14 months ago by b.nota ♦ 4.0k
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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 16 months ago by gundalav • 240
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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 16 months ago by gundalav • 240

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