AlignmentsTrack empty plot
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0
Entering edit mode
karlaarz • 0
@karlaruizce30-23403
Last seen 4 weeks ago
Italy

Hello all,

I am trying to add the "AlignmentsTrack" as coverage and sashimi plot using one of my bam files. However, I get an empty plot as an output.

I've tried using "DataTrack" instead, playing with the max.height and min.height parameters and reinstalling the package but nothing worked. My code is:

#set genome and chromosome
gen <- 'hg38'
chr <- 'chr1'

afrom=93438921
ato=93565861

b1<- 'mysample.bam'

#genome axis track
gtrack <- GenomeAxisTrack()

#ideogram track
itrack <- IdeogramTrack(genome = gen, chromosome = chr)

#TxDb object
txdb <- makeTxDbFromGFF(file="assembled.gtf",
                        organism="Homo sapiens", format = "gtf")
#gene track
grtrack <- GeneRegionTrack(txdb,
                           genome = gen,
                           chromosome = chr,
                           fill='black',
                           transcriptAnnotation = "symbol",
                           name = "gene", background.title = "darkblue", exon = ex, stacking = 'squish')


alTrack <- AlignmentsTrack(range = b1, name = 'data', type= "coverage", 
                           isPaired = TRUE, genome = gen, chromosome = chr)

plotTracks(c(itrack, gtrack, alTrack, grtrack), from = afrom , to = afrom, chromosome = chr,
           type = c("coverage", "sashimi"))

enter image description here

Do you have any idea why this could be happening?

Thanks

Coverage RNASeq plot Gviz • 117 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 17 hours ago
United States

Is your 'ato' object intended to be a negative number?

0
Entering edit mode

No, it was my mistake while copying the script, but the output is still the same. I've already edited the post by removing the negative symbol.

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