User: Jiping Wang

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Jiping Wang70
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Posts by Jiping Wang

<prev • 17 results • page 1 of 2 • next >
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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 13 days 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 18 days 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 18 days ago by Jiping Wang70 • updated 18 days 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 weeks ago by Jiping Wang70
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Comment: C: readGAlignmentPairs fail to read paired end data
... Yes, it's from SRA. Thanks for help. ...
written 5 weeks ago by Jiping Wang70
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Comment: C: readGAlignmentPairs fail to read paired end data
... Hi Martin, Thanks so much for such detailed guidance and help! It seems to be working now. I will further try whether the output from the paired alignment file will lead to right coverage score calculation on transcript/genes. ``` > bf = BamFile("SRR873822.bam", asMates = TRUE, qnameSuffixS ...
written 5 weeks ago by Jiping Wang70
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Comment: C: readGAlignmentPairs fail to read paired end data
... Thanks, Martin! This is very helpful. I think we are close to the answer why I couldn't get the paired-end count. Indeed the qname of the two mates have the extension .1 and .2. For example, the following are two paired ends. I thought this is the standard for naming the two mates and the R package ...
written 5 weeks ago by Jiping Wang70
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Comment: C: readGAlignmentPairs fail to read paired end data
... Thanks again! Still I cannot get the paired end counts. ``` > bf = BamFile("SRR873822.bam", asMates = TRUE) > param = ScanBamParam(which = gr["chr1"]) > readGAlignmentPairs(bf, param = param) GAlignmentPairs object with 0 pairs, strandMode=1, and 0 metadata columns: seqnames strand : ...
written 5 weeks ago by Jiping Wang70
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Comment: C: readGAlignmentPairs fail to read paired end data
... I do not quite understand the output of quckBamFlagSummary. What does it tell about the paired-end or single-end? ``` > Rsamtools::quickBamFlagSummary(bf, param = param) group | nb of | nb of | mean / max of | records | ...
written 5 weeks ago by Jiping Wang70
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Comment: C: readGAlignmentPairs fail to read paired end data
... Hi Martin, Thanks so much for help. My data is paired-end RNA-seq data, aligned using tophat. I followed your recommendation, here is what got: ``` > bf = BamFile("SRR873822.bam") > gr = as(seqinfo(bf), "GRanges") > chr1 = gr[1] ## or maybe gr["chr1"] > idxstatsBam(bf) seqnames ...
written 5 weeks ago by Jiping Wang70

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