[BioC] BitSeq input data error

[Fatemehsadat Seyednasrollah]

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