Closed komalsrathi closed 6 years ago
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 :)
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.
plotFusion
, I got a plot like this before:
plotFusion(
fusion = fusion,
bamfile = bamfile,
edb = edb,
nonUCSC = TRUE,
reduceTranscripts = TRUE)
Thank you for providing everything!:) I will look at this over the weekend.
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!:)
Can this too be closed, @komalsrathi?
I am testing this today and will close this asap. Thanks!!
On Wed, Oct 25, 2017 at 11:25 AM Stian Lågstad notifications@github.com 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 https://github.com/stianlagstad/chimeraviz/issues/5#issuecomment-339368165, 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 | rathik@email.chop.edu
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!
Hi,
I have successfully been able to follow all steps from the chimeraviz manual until
plotFusionTranscript
. When I run it, it gives me the following error:These are the steps I followed:
This is how the reference fasta
referenceFilename
looks like:These are first few lines of the fastq files:
bamfile
usingrsubreadAlign
:And the bam file looks like this - again not sure what is
chrNA
doing in the header or in the alignments:Any help would be much appreciated. Thanks!!