User: seungjoon.kim

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Posts by seungjoon.kim

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Rsamtools: system.file no file found
... Thanks for the advice. Specify the path to the file works well in analyzing overlap between Bam file and gene model  but I want to sort reads into groups by start position and system.file and Rsamtools gives me empty file. bam <- readGAlignments("Aligned.out.sorted.bam") It gives this result: ...
written 7 weeks ago by seungjoon.kim0
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Answer: A: readCufflinks problem with extdata
... Hi I just installed cummeRbund and also have exactly the same issue with 50 or more warnings. CuffSet instance with: 0 samples 0 genes 0 isoforms 0 TSS 0 CDS 0 promoters 0 splicing 0 relCDS Seems not just my problems   ...
written 8 weeks ago by seungjoon.kim0
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Comment: C: Isoforms detection using bioconductor
... Thanks for the comment. it works well with analyzing isoforms but still has problem when plotting the results. When I followed this script: par(mfrow = c(2,1), mar = c(2,2,1,2), pty = "m") plotSpliceGraph(rowRanges(sgfc_pred), geneID = 1, toscale = "none", color_novel = "red") for (j in 1:4){   p ...
written 8 weeks ago by seungjoon.kim0
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Comment: C: IRanges from BAM file to GRanges convert
... I solved the problem by changing into data frame and making Granges object. bam <- readGAlignments("file.bam") bam2 <- as.data.frame(bam) # data frame to GRanges (Test) bam2.GR <- GRanges(seqnames = bam2$seqnames, ranges=IRanges(start = bam2$start, end = bam2$end),                    str ...
written 8 weeks ago by seungjoon.kim0
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Comment: C: Isoforms detection using bioconductor
... In the beginning, I found this kind of error. > bamPath <- "/data/murphy/home/XXX/XXX/sorted_ccs.bam" > bamFile <- BamFile(bamPath) > getBamInfo(bamFile) Error: sample_info must be a data frame with columns sample_name, file_bam In this case, how can I add sample_name? Also, I u ...
written 9 weeks ago by seungjoon.kim0
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Comment: C: Isoforms detection using bioconductor
... Thanks. I will try it. ...
written 9 weeks ago by seungjoon.kim0
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IRanges from BAM file to GRanges convert
... Hi there, I have a problem with change IRanges object to GRanges. > test_bam_Iranges IRangesList of length 1 [[1]] IRanges object with 8 ranges and 0 metadata columns: start end width <integer> <integer> <integer> [1] 14404 14829 426 ...
iranges granges written 9 weeks ago by seungjoon.kim0
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Comment: C: Isoforms detection using bioconductor
... Thanks for the advice. So I tried to use SGSeq to analyze data and some questions and errors came out. I tried to follow the method in splice-variant-identification written by Leonard D Goldstein and how do you retrieve GRanges object of FBXO31 gene. Because it is possible to retrieve a certain chro ...
written 9 weeks ago by seungjoon.kim0
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Comment: C: Rsamtools: system.file no file found
... Thank you!!! It works well. But a question comes out. Then, why people do bamPath <- system.file("extdata", "sorted_file.bam", package = "Rsamtools", mustWork = TRUE) instead of bamPath <- "c:/Users/mtmorgan/my_data/sorted_file.bam" Because the latter one seems more short and convenience ...
written 10 weeks ago by seungjoon.kim0
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Rsamtools: system.file no file found
... Hi, I am watching Rsamtools in Coursera and I want to get Bam file to R so I used system.file and Rsamtools. So when I ran this command: bamPath <- system.file("extdata", "sorted_file.bam", package = "Rsamtools", mustWork = TRUE) It gives me error with message no file found. w/o mustWork, it ...
rsamtools bam file written 10 weeks ago by seungjoon.kim0 • updated 10 weeks ago by Martin Morgan ♦♦ 20k

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