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BIMSBbioinfo / ciRcus

An R package for annotation of circular RNAs
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Output from find_circ error #6

Closed BaluPai closed 7 years ago

BaluPai commented 8 years ago

I have been using find_circ v1.2 for generating my cirRNA result file. But I get the following error message when using my files, whereas the test data runs are okay.

circs.f <- annotateCircs(circs.bed = "C:/Users/Balu/Desktop/sample_circ_candidates.bed",
                         annot.list = annot.list,
                         assembly = "hg19")
Error in validObject(.Object) : 
  invalid class “GRanges” object: 'x@elementMetadata' is not parallel to 'x'

There are a few differences among the files:

  1. There is no spliced_at_end column in the new version output.
  2. Small differences in category column terms like, PERFECT instead of PERFECT_EXT etc.

The sample file is after filtering using grep.

Any help/suggestions would be appreciated.

Regards, Balu

edit (@mschilli87): formatting

retaj commented 8 years ago

Dear Balu,

As you noticed, some columns were added (or changed names) in find_circ v1.2. It is fixed now in ciRcus, just update the package to v0.1.1

Best regards, Petar

BaluPai commented 8 years ago

Dear Petar, I tried the new version over the weekend and seems to work fine. Thanks. But another issue that I worked around is the code in annotate.R.

During the gtf2sqlite I have been getting this error:

gtf2sqlite(assembly = c("hg19"),
           db.file = "hg19.sqlite")
updating AnnotationHub metadata: retrieving 1 resource
  |=============================================================================| 100%
snapshotDate(): 2016-01-25
require(“GenomicRanges”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/10684’
retrieving 1 resource
  |=============================================================================| 100%
using guess work to populate seqinfo
Error in keepStandardChromosomes(gtf.gr) : 
  Cannot determine standard chromosomes, Specify species arg_

I have been working around by deleting the code for this part in annotate.R:

gtf.gr <- keepStandardChromosomes(gtf.gr)

Thanks.

best regards, Balu

edit (@mschilli87): formatting

mschilli87 commented 7 years ago

@BaluPai: If this is still an issue, can you please post the output of seqinfo for your GRanges?

mschilli87 commented 7 years ago

Closing as I cannot reproduce the issue (with current version) and thus assume it was fixed in the meantime.

@BaluPai: Feel free do re-open if you still have this issue after re-installing ciRcus.