Question: ASpli ERROR during the counting step
1
gravatar for daniele.ottaviani
18 months ago by
daniele.ottaviani10 wrote:

 

Hi,

I'm trying to perform diff. splicing analysis and novel exon discovery on my RNAseq data using the ASpli package.

I loaded my .bam files with:

> bam <- loadBAM(targets)

...but then R gives an error while performing the counting step:

> counts <- readCounts ( features, bam, targets, cores = 4, readLength = 126, maxISize = 50000, minAnchor = NULL )

ead summarization by gene completed
Read summarization by bin completed
Error in x@start[] <- S4Vectors:::numeric2integer(value) : 
  replacement has length zero

Does anyone have any advise about where the error is coming from or how to solve it?

Many thanks in advance for helping!

Daniele

 

 

 

 

 

rnaseq aspli • 415 views
ADD COMMENTlink modified 14 months ago by hojka.anna10 • written 18 months ago by daniele.ottaviani10
Answer: ASpli ERROR during the counting step
1
gravatar for hojka.anna
14 months ago by
hojka.anna10
hojka.anna10 wrote:

Hi!

I noticed the same problem as Daniel, when I tried to use ASpli. When I noticet that problem with my data I tried on example data adn problem is the same

Here is my sesion with example data

> annFile       <- aspliExampleGTF()
> aTxDb         <- makeTxDbFromGFF(annFile)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> symbols       <- data.frame( row.names = genes( aTxDb ),
+ symbol = paste( 'This is symbol of gene:',
+ genes( aTxDb ) ) )
> features      <- binGenome( aTxDb, geneSymbols = symbols )
* Number of extracted Genes = 10
* Number of extracted Exon Bins = 38
* Number of extracted intron bins = 34
* Number of extracted trascripts = 25
* Number of extracted junctions = 23
* Number of AS bins (not include external) = 17
* Number of AS bins (include external) = 17
* Classified as:
        ES bins = 1     (6%)
        IR bins = 3     (18%)
        Alt5'ss bins = 2        (12%)
        Alt3'ss bins = 2        (12%)
        Multiple AS bins = 9    (53%)
        classified as:
                        ES bins = 1     (11%)
                        IR bins = 4     (44%)
                        Alt5'ss bins = 2        (22%)
                        Alt3'ss bins = 1        (11%)

> bamFiles <- c( "Ct1.bam", "Ct2.bam", "Mut1.bam","Mut2.bam" )
> targets <- data.frame( row.names =  c("CT_rep1","CT_rep2", "Mut_rep1", "Mut_rep2"),
+                        bam = bamFiles,
+                        genotype = c("CT","CT", "Mut", "Mut") ,
+                        stringsAsFactors = FALSE )
> targets <- aspliTargetsExample()
> bam <- loadBAM(targets)
> counts <- readCounts (
+      features,
+      bam,
+      targets,
+      cores = 1,
+      readLength=100,
+      maxISize = 50000,
+      minAnchor = NULL )
Read summarization by gene completed
Read summarization by bin completed
Error in x@start[] <- S4Vectors:::numeric2integer(value) :
  replacement has length zero
> as <- AsDiscover( counts, targets, features, bam, readLength=100L,
+ threshold = 5)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function 'AsDiscover' for signature '"standardGeneric"'
>

Any advice on that?

Anna

ADD COMMENTlink written 14 months ago by hojka.anna10
Answer: ASpli ERROR during the counting step
0
gravatar for emancini
17 months ago by
emancini10
emancini10 wrote:

Dear Daniela, 

Could you post your sessionInfo() please?

It this error present when you run the code using the example data?

Thanks!

 

ADD COMMENTlink written 17 months ago by emancini10
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