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Question: IRanges error while input rsem data into ballgown : .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
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gravatar for kicheol.kim
3 months ago by
kicheol.kim0 wrote:

I am trying to input ballgown object from rsem count using ballgownrsem function. But it's not working with this error. How I can solve this problem? I used gtf file from GenCode r28. I also downloaded from UCSC table browser, but still shows same error.

 

> bg <- ballgownrsem(dir = "dir_rsemcount", rsem.files, gtf=file.path("C:/Users/kicheol/Desktop/Projects/FutureMS/Analysis/ucsc.gencodeV28.comprehensive.gtf"), UCSC = TRUE, tfield = "transcript_id", bamout = "none", pData = sTable, verbose = TRUE, meas = "all", zipped = FALSE)
Thu Jul 05 21:41:24 2018
Thu Jul 05 21:41:25 2018: reading annotation
Thu Jul 05 21:43:43 2018: handling exons
Thu Jul 05 21:44:13 2018: handling introns
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 16585: negative widths are not allowed

 

> traceback()
6: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
5: solveUserSEW0(start = start, end = end, width = width)
4: IRanges(start = end(unltrans)[notLast] + 1, end = start(unltrans)[which(notLast) + 
       1] - 1)
3: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, 
       strand = strand, mcols = mcols, seqlengths = seqlengths, 
       seqinfo = seqinfo)
2: GRanges(seqnames = seqnames(unltrans)[notLast], ranges = IRanges(start = end(unltrans)[notLast] + 
       1, end = start(unltrans)[which(notLast) + 1] - 1), strand = strand(unltrans)[notLast])
1: ballgownrsem(dir = "C:/Users/kicheol/Desktop/Projects/FutureMS/Analysis/results/illumina/RSEM", 
       sTable_nSeq$fileID, gtf = file.path("C:/Users/kicheol/Desktop/Projects/FutureMS/Analysis/ucsc.gencodeV28.comprehensive.gtf"), 
       UCSC = TRUE, tfield = "transcript_id", bamout = "none", pData = sTable_nSeq, 
       verbose = TRUE, meas = "all", zipped = FALSE)

 

ADD COMMENTlink modified 12 weeks ago • written 3 months ago by kicheol.kim0
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