Comments (7)
I think the problem is the bamfile you're using: bamfile <- 'fusionAlignment.bam'
. This is the bamfile containing reads aligned to the sequence around the fusion breakpoint. This is the correct bamfile to use for the plotFusionReads
plot. But the bamfile you need for the plotFusion
, plotTranscripts
, and plotFusionTranscript
is the original bamfile used with the fusion finder (i.e. the one with all sequencing reads aligned to the whole genome). Does that make any sense?
And BTW: This is a perfect timing for any suggestions on how I can make chimeraviz better or more intuitive, since a new Bioconductor release is just around the corner. Any feedback is welcome!:)
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Thank you for your interest in chimeraviz! Could you by any chance share your input files? At first glance I think it might have to do with different chromosome naming ("chr11" vs. just "11"), though I can't investigate it further right now. I'll take a closer look as soon as I can.
Sidenote: The reason "chrNA" is used (chimeraviz sets this in the writeFusionReference
function) is to make Gviz (the library used for most visualizations) happy. And since we're looking at the fusion sequence, which might be partly from different chromosomes, "chrNA" sort of makes sense :)
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Hi Stian,
Thanks for the response. Here is the google drive link with all the data - input fastq files, reference fasta generated by writeFusionReference
, Ensembl GTF modified with "chr", bam files generated using writeFusionReference
as well as fusion catcher output folder. Also attaching my R script in the drive so you can reproduce the output.
https://drive.google.com/open?id=0B-8gQV1WZcYdQXUyNFF6UEF1bnM
I am not sure what happened within the last couple of hours but now I am stuck at an upstream step which had worked for me before.
- For
plotFusion
, I got a plot like this before:
plotFusion(
fusion = fusion,
bamfile = bamfile,
edb = edb,
nonUCSC = TRUE,
reduceTranscripts = TRUE)
But now I am getting a plot like this which looks like some graphics issue:
- The basic
plotTranscripts
function still looks ok:
plotTranscripts(
fusion = fusion,
edb = edb)
- But
plotTranscripts
with bam file input does not show any coverage:
plotTranscripts(
fusion = fusion,
edb = edb,
bamfile = bamfile,
nonUCSC = TRUE, reduceTranscripts = T)
- And
plotFusionTranscript
is giving me an error:
plotFusionTranscript(fusion = fusion,
edb = edb,
bamfile = bamfile)
Error in .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file), :
seqlevels(param) not in BAM header:
seqlevels: 'chr11'
file: fusionAlignment.bam
index: fusionAlignment.bam.bai
This is my sessionInfo:
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] chimeraviz_1.2.2 ensembldb_2.0.4 AnnotationFilter_1.0.0
[4] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2 Biobase_2.36.2
[7] Gviz_1.20.0 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3
[10] Biostrings_2.44.2 XVector_0.16.0 IRanges_2.10.5
[13] S4Vectors_0.14.7 BiocGenerics_0.22.1 BiocInstaller_1.26.1
loaded via a namespace (and not attached):
[1] ProtGenerics_1.8.0 bitops_1.0-6
[3] matrixStats_0.52.2 bit64_0.9-7
[5] RColorBrewer_1.1-2 httr_1.3.1
[7] rprojroot_1.2 tools_3.4.2
[9] backports_1.1.1 R6_2.2.2
[11] DT_0.2 rpart_4.1-11
[13] Hmisc_4.0-3 DBI_0.7
[15] lazyeval_0.2.0 colorspace_1.3-2
[17] nnet_7.3-12 gridExtra_2.3
[19] bit_1.1-12 curl_3.0
[21] compiler_3.4.2 htmlTable_1.9
[23] DelayedArray_0.2.7 rtracklayer_1.36.5
[25] scales_0.5.0 checkmate_1.8.4
[27] readr_1.1.1 RCircos_1.2.0
[29] stringr_1.2.0 digest_0.6.12
[31] Rsamtools_1.28.0 foreign_0.8-69
[33] rmarkdown_1.6 base64enc_0.1-3
[35] dichromat_2.0-0 pkgconfig_2.0.1
[37] htmltools_0.3.6 BSgenome_1.44.2
[39] htmlwidgets_0.9 rlang_0.1.2
[41] RSQLite_2.0 shiny_1.0.5
[43] BiocParallel_1.10.1 acepack_1.4.1
[45] VariantAnnotation_1.22.3 RCurl_1.95-4.8
[47] magrittr_1.5 GenomeInfoDbData_0.99.0
[49] Formula_1.2-2 Matrix_1.2-11
[51] Rcpp_0.12.13 munsell_0.4.3
[53] stringi_1.1.5 yaml_2.1.14
[55] SummarizedExperiment_1.6.5 zlibbioc_1.22.0
[57] org.Hs.eg.db_3.4.1 plyr_1.8.4
[59] AnnotationHub_2.8.2 blob_1.1.0
[61] lattice_0.20-35 splines_3.4.2
[63] hms_0.3 knitr_1.17
[65] biomaRt_2.32.1 XML_3.98-1.9
[67] evaluate_0.10.1 biovizBase_1.24.0
[69] latticeExtra_0.6-28 data.table_1.10.4-1
[71] httpuv_1.3.5 gtable_0.2.0
[73] ggplot2_2.2.1 mime_0.5
[75] xtable_1.8-2 survival_2.41-3
[77] tibble_1.3.4 GenomicAlignments_1.12.2
[79] memoise_1.1.0 cluster_2.0.6
[81] interactiveDisplayBase_1.14.0 BiocStyle_2.4.1
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Thank you for providing everything!:) I will look at this over the weekend.
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Can this too be closed, @komalsrathi?
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I am closing this as I did not get this error with the latest test I did on a different sample. Thanks for all the help!
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Related Issues (20)
- Question: what are the red bands on the chromosome? HOT 4
- Assignment to global environment HOT 1
- plot_fusion function not finding "SPFQ" or "CADM2" transcripts in an edb object that has them. HOT 2
- Why is it impossible to use plot_fusion_transcript_with_protein_domain without a BAM file? HOT 1
- Support ChimPipe HOT 1
- coverage issue in plot_fusion_separate HOT 2
- How to make fusioncatcher data compatible to chimeraviz HOT 4
- Chromosome not labeled correctly? HOT 4
- Support Fusion-Bloom
- Travis build fails
- plot_fusion_transcript_with_protein_domain(): error plotting upstream domains HOT 2
- Failed to create reference fasta file HOT 4
- How to input STAR-SEQR output? HOT 1
- Dependency on deprecated ArgumentCheck CRAN package HOT 1
- 2 question with chimeraviz HOT 3
- Custom genomes HOT 2
- Error during the execution of plot_fusion HOT 5
- Failed to create EnsDb HOT 1
- No coverage data for plot_fusion HOT 2
- Fusion transcript plot with protein domain annotations HOT 1
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