seqlevels(param) not in BAM header about chimeraviz

[stianlagstad]

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!:)

[komalsrathi]

I am testing this today and will close this asap. Thanks!!

On Wed, Oct 25, 2017 at 11:25 AM Stian Lågstad ***@***.***> wrote: Can this too be closed, @komalsrathi <https://github.com/komalsrathi>? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGrSJ-dgGHAffF7pGkT_VnqpRHO0xNO0ks5sv1L5gaJpZM4P2bV5> .

-- *Komal S Rathi* | Bioinformatics Scientist II, DBHi, The Children's Hospital of Philadelphia | [email protected]

[stianlagstad]

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 :)

[komalsrathi]

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.

1. 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:

2. The basic plotTranscripts function still looks ok:

plotTranscripts(
  fusion = fusion,
  edb = edb)

3. But plotTranscripts with bam file input does not show any coverage:

plotTranscripts(
  fusion = fusion,
  edb = edb,
  bamfile = bamfile,
  nonUCSC = TRUE, reduceTranscripts = T)

4. 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 

[stianlagstad]

Thank you for providing everything!:) I will look at this over the weekend.

[stianlagstad]

Can this too be closed, @komalsrathi?

[komalsrathi]

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!