hi Kaj, I think there is too problems here actually. As of yet, ChIPQC does not accept TxDB directly, please see this thread to create your own annotation. creating custom genome annotation for the ChIPQC package. <https: support.bioconductor.org="" p="" 70893=""/>Not entirely sure how your version is working but will test this out. We have the code to use TxDB directly and will include in the next version. Hopefully the instructions in thread will explain. The second problem i think is unrelated to the warnings but in summit identification. This looks too have occurred when ChIP is looking for peak summits but here you are providing the MACs output for peak summits directly which could have caused a problem. Does the problem occur when using the actual peaks.bed file? Could you share the *summits.bed and *peaks.bed with me privately at tc.infomatics@gmail.com and i can take look and try and recreate the issue. best, tom On Thu, Jun 1, 2017 at 6:50 PM, tofukaj [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User tofukaj <https: support.bioconductor.org="" u="" 9928=""/> wrote Question: > ChIPQC gives Error subscript contains out-of-bounds ranges with custom > transcript database <https: support.bioconductor.org="" p="" 96555=""/>: > > Dear Great Helpers, > > I've tried 'ChIPQC' package with chip-seq data of the cow. I've created > the annotation TxDb from 'gtf' file acquired from ensembl. The codes and > results are as following: > > R > library(GenomicRanges) > library(GenomicFeatures) > library(ChIPQC) > > # Create TxDb annotation > btaurus_txdb <- makeTxDbFromGFF('Bos_taurus.UMD3.1.89.gtf.gz') > > # Determine locations of bam and bed files > btaurus_txdb <- loadDb(file="btaurus_txdb.sqlite") > bamFile <- file.path(maindir, "macs2/bowtie2/SRR1977480.sorted.bam") > bedFile <- file.path(maindir, "macs2/bowtie2/SRRSRR1977480K4peak_summits.bed") > > # ChIPQC analysis > exampleExp <- ChIPQCsample(bamFile, peaks=bedFile, annotation=list(btaurus_txdb), chromosomes=NULL) > > By the script provided above, I've got the results and errors as following: > > Removing 2 chromosomes with length less than cross-coverage shift > Bam file has 3315 contigs > Calculating coverage histogram for 1 > > Calculating SSD for 1 > > Calculating unique positions per strand for 1 > > Calculating shift for 1 > > 300 / 300 > Counting reads in features for 1 > > Signal over peaks for 1 > > done > Calculating coverage > Calculating Summits on 1 ..Calculating coverage histogram for 10 > > Calculating SSD for 10 > > Calculating unique positions per strand for 10 > > Calculating shift for 10 > > 300 / 300 > Counting reads in features for 10 > > Signal over peaks for 10 > > done > Calculating coverage > Calculating Summits on 10 ..Calculating coverage histogram for 11 > > Calculating SSD for 11 > > Calculating unique positions per strand for 11 > > Calculating shift for 11 > > 300 / 300 > Counting reads in features for 11 > > Signal over peaks for 11 > > done > Calculating coverage > Calculating Summits on 11 ..Error: subscript contains out-of-bounds ranges > In addition: Warning messages: > 1: In BioC 3.5, the 'force' argument was replaced by the more flexible > 'pruning.mode' argument, and is deprecated. See ?seqinfo for the > supported pruning modes. Note that 'force=TRUE' is equivalent to > 'pruning.mode="coarse"'. > 2: In BioC 3.5, the 'force' argument was replaced by the more flexible > 'pruning.mode' argument, and is deprecated. See ?seqinfo for the > supported pruning modes. Note that 'force=TRUE' is equivalent to > 'pruning.mode="coarse"'. > 3: In BioC 3.5, the 'force' argument was replaced by the more flexible > 'pruning.mode' argument, and is deprecated. See ?seqinfo for the > supported pruning modes. Note that 'force=TRUE' is equivalent to > 'pruning.mode="coarse"'. > 4: In BioC 3.5, the 'force' argument was replaced by the more flexible > 'pruning.mode' argument, and is deprecated. See ?seqinfo for the > supported pruning modes. Note that 'force=TRUE' is equivalent to > 'pruning.mode="coarse"'. > > Would you please help me figure out what is happening and how to fix it > properly? I must confess that I'm just the starter in this field with very > poor experience. If my question is not properly managed, I would like to > apologize you all in advance. > > Best Regards, > Kaj > > sessionInfo() > R version 3.4.0 (2017-04-21) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.2 LTS > > Matrix products: default > BLAS: /usr/lib/libblas/libblas.so.3.6.0 > LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=th_TH.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=th_TH.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=th_TH.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=th_TH.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] rtracklayer_1.36.2 ChIPQC_1.12.0 > [3] DiffBind_2.4.2 SummarizedExperiment_1.6.1 > [5] DelayedArray_0.2.4 matrixStats_0.52.2 > [7] ggplot2_2.2.1 GenomicFeatures_1.28.0 > [9] AnnotationDbi_1.38.0 Biobase_2.36.2 > [11] GenomicRanges_1.28.2 GenomeInfoDb_1.12.0 > [13] IRanges_2.10.1 S4Vectors_0.14.1 > [15] BiocGenerics_0.22.0 > > ------------------------------ > > Post tags: chipqc > > You may reply via email or visit ChIPQC gives Error subscript contains out-of-bounds ranges with custom transcript database >