JesusMHU
commented
1 year ago Also, if I treat it as SE, I get this error during a subsequent step.
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="SE", strandMode=0) #unstranded
Junctions PJU completed
Junctions PIR completed Junctions IR PIR completed
Junctions AltSS PSI completed Junctions ES PSI completed Warning messages: 1: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''. 2: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''. 3: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''. 4: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''. 5: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''. 6: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''.
gb <- gbDUreport(gbcounts, contrast = c(-1,1)) Filtering genes: Filtering by reads. Filtering using control,treatment conditions Filtering any condition with mean minimum value 10 Filtering by read density. Filtering using control,treatment conditions Filtering any condition with mean minimum value 0.05 Filtering genes done Genes differential expression: Contrast:-1control 1treatment Running GLM LRT Genes differential expression done Genes DE completed Bins DE completed jdur <- jDUreport(asd, contrast=c(-1,1)) Running junctionsPJU test Running junctionsPIR test Running irPIR test Running esPSI test Running altPSI test Error in
.rowNamesDF<-(x, value = value) : invalid 'row.names' length sr <- splicingReport(gb, jdur, counts=gbcounts) Error in .hasSlot(jdu, ".ASpliVersion") : object 'jdur' not found is <- integrateSignals(sr,asd, bin.FC=1) Error in h(simpleError(msg, call)) : error in evaluating the argument 'sr' in selecting a method for function 'integrateSignals': object 'sr' not found exportSplicingReports(sr, output.dir="2.sr_1h") Error in h(simpleError(msg, call)) : error in evaluating the argument 'sr' in selecting a method for function 'exportSplicingReports': object 'sr' not found exportIntegratedSignals(is,sr=sr, output.dir = "2.SplicingReport_1h", counts=gbcounts,features=features,asd=asd, mergedBams = mBAMs) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'exportIntegratedSignals' for signature '"function"'
estepi
Hi! I hope you're doing great.
I'm opening this issue regarding a JCounts Error when analyzing BAM files of S. lycopersicum data. Here's the error:
BAMFiles <- c("Control_1.bam","Control_2.bam", "Control_3.bam", "NaCl_1h_1.bam", "NaCl_1h_2.bam", "NaCl_1h_3.bam") targets <- data.frame(row.names = paste0('Sample',c(1:6)),
mBAMs <- data.frame( bam = c("Control_sorted.bam", "NaCl_1h_sorted.bam"),
gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 18, maxISize = 50000, libType="PE", strandMode=0) Summarizing Sample1 ETA: 43 min Summarizing Sample2 ETA: 35 min Summarizing Sample3 ETA: 26 min Summarizing Sample4 ETA: 20 min Summarizing Sample5 ETA: 11 min Summarizing Sample6 ETA: 0 min There were 12 warnings (use warnings() to see them)
asd <- jCounts(counts=gbcounts, features=features, minReadLength=18, libType="PE", strandMode=0) #unstranded Junctions PJU completed Error in .local(x, use.names, use.mcols, ...) : For some pairs in 'x', the 2 alignments are not on the same chromosome. Cannot associate a unique genomic range to such pairs. Please call granges() with 'on.discordant.seqnames="drop"' to drop these pairs, or with 'on.discordant.seqnames="split"' to represent each of them with 2 genomic ranges in the returned GRanges object. Note that in both cases the returned object won't be parallel to 'x'. Alternatively, please consider using grglist() instead of granges() to turn 'x' into a GRangesList object instead of a GRanges object. See ?GAlignmentPairs for more information. In addition: Warning messages: 1: In .make_GAlignmentPairs_fromGAlignments(gal, strandMode = strandMode, : 24899 alignments with ambiguous pairing were dumped. Use 'getDumpedAlignments()' to retrieve them from the dump environment. 2: In FUN(X[[i]], ...) : Some seqnames had a '.' present in their names. ASpli had to normalize them using ''.
I read that you can either treat the data as SE (and I'm not sure which would be the implications, whether I should or not do it with my data) or that I could try to remove/drop these in the alignment step (I use Hisat, and I'm not sure how to drop it). Can you give me any insight on this issue? Or any advice?
Thanks a lot in advance!!
My session info, just in case:
R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] compiler_3.6.3