User: Jiping Wang

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Jiping Wang70
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Posts by Jiping Wang

<prev • 23 results • page 1 of 3 • next >
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Comment: C: exonsBy does not order exons by ascending rank, is it a bug or outdated document
... Thanks. I had another post earlier, in which you basically have helped me out in the same way(very grateful). It worked. I want to follow the IntersectionStrict mode as HTSeq requires to calculate the coverage curve. if one read align to both genes (i.e. genes may overlap), that read should not be c ...
written 21 days ago by Jiping Wang70
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Comment: C: exonsBy does not order exons by ascending rank, is it a bug or outdated document
... That makes sense. I will give it a try. Thanks again for great help! But there is one potential issue: if a read partially overlaps with an exons, that will be counted in the coverage score? I need to judge whether a read or a pair of reads are compatible with the features (exons for the same gene) ...
written 22 days ago by Jiping Wang70
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Comment: C: exonsBy does not order exons by ascending rank, is it a bug or outdated document
... I am not to distinguish between different transcripts as it's just not possible to deconvolve them based on reads count. The reads count from different splicing forms will be just piled up, and repeatedly counted on the shared axons if we do the coverage for transcripts. Instead I am listing all exo ...
written 22 days ago by Jiping Wang70
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Comment: C: exonsBy does not order exons by ascending rank, is it a bug or outdated document
... Thanks so much! I indeed ignored the fine details under exonsBy. Is there a quick way to sort exon in ascending rank if they are on minus strand? It takes extremely long time if I do the following: ``` for(i in 1:length(all_genes)){ if(runValue(strand(all_genes[[i]]))=="-"){ all_genes[[i]] ...
written 23 days ago by Jiping Wang70
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exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
... I tried to use *coverageByTranscript* function from GenomicAlignments package to calculate the RNA-seq coverage along transcripts. This function requires the exons be sorted in ascending rank (i.e. the first Exxon in the transcript should be listed in the GRanges object first, and so forth, see refe ...
genomicfeatures genomicalignments coveragebytranscript genomicalignment exonby written 23 days ago by Jiping Wang70 • updated 23 days ago by Hervé Pagès ♦♦ 14k
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Rsamtools: how to extract uniquely aligned single-end or paired-end by ScanbamParam
... A quick question: is there any way to extract uniquely aligned single-end or paired-end reads using Rsamtools? I read carefully about the documentation and did find a clear clue. *IsSecondaryAlignment=T* tag does not exclude a read which had aligned to multiple locations we designated as *primary* a ...
rsamtools written 3 months ago by Jiping Wang70 • updated 3 months ago by Martin Morgan ♦♦ 24k
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Comment: C: coverageByTranscript coudble counts overlapped region for paired-end data
... Thanks so much. I also figured out the *reduce* function as well. Very grateful for your detailed help! ...
written 4 months ago by Jiping Wang70
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Comment: C: coverageByTranscript coudble counts overlapped region for paired-end data
... Hi Hervé, Thanks for your quick help. I understand and appreciate what you explained. I am just wondering whether your package could implement this as default for the paired-end data. I saw there are some other posts where users raised the same question. In my opinion, the coverage calculation f ...
written 4 months ago by Jiping Wang70
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coverageByTranscript coudble counts overlapped region for paired-end data
... I have a paired-end RNA-seq data in bam. It was read into R using readGAlignmentPairs, named gal2. The compatible reads pairs was parsed using findCompatibleOverlaps function. The following codes only specifically examines compatible read pairs for 4th gene in the dm3_transcripts list. There was onl ...
genomicalignments rna-seq paired-end read coverage written 4 months ago by Jiping Wang70 • updated 4 months ago by Hervé Pagès ♦♦ 14k
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Why extractList fails to relist paired-end RNA-seq data when using pcoverageByTranscript?
... I am trying to use pcoverageByTranscript function to calculate coverage score on each genes. I have a paired-end RNA-seq data. I read in with readGAlignments function as gal1 and readGAlignmentPairs function as gal2 separately. ``` > which <- GRanges(seqnames = c("chr1")) > gr = as(seqinf ...
genomicalignments pakcage extractlist written 4 months ago by Jiping Wang70

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