[BioC] BitSeq input data error

[Peter Glaus]

Dear Fatemehsadat,
this particular error report in version 1.0.1 of BitSeq is a bit 
ambiguous, so please try updating to the newest version of BitSeq.

Most probably the error is caused by the number of transcripts in BAM 
file being different from the number in reference Fasta (25 vs 5927492). 
What kind of reference are you using? BitSeq expects the reference to be 
assembled transcriptome (one Fasta entry is one entire transcript), and 
you don't need TopHat to align reads to this kind of reference.

Regards,
Peter Glaus.

On 11/05/12 17:28, Fatemehsadat Seyednasrollah wrote:
> Hi all,
>
> I want to use SamBit to get the DE genes of my dataset. I have used TopHat to map my data. As far as I understand BitSeq needs to input files: The BAM/SAM file and the fasta file. I used the accepted_hits.bam file from TopHat and the fasta file I have used to map but I got error in the first line of my code. Below is the code and the error I received. Any suggestions to fix it? many thanks in advance.
>
> res1 <- getExpression("accepted_hits.bam", "sample.fasta", log=TRUE,MCMC_burnIn=200, MCMC_samplesN=200, MCMC_samplesSave=50)
>
> and the error:
> Error in parseAlignment(alignFile, probF, trSeqFile, trInfoFile = trF,  :
>    Main: number of transcripts don't match: 25 vs 5927492
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BitSeq_1.0.1         zlibbioc_1.2.0       Rsamtools_1.8.6
> [4] Biostrings_2.24.1    GenomicRanges_1.8.13 IRanges_1.14.4
> [7] BiocGenerics_0.2.0   BiocInstaller_1.4.9
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.2 stats4_2.15.1  tools_2.15.1
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