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