[BioC] BitSeq input data error

[Fatemehsadat Seyednasrollah]

Dear Peter,

So many thanks for the reply. First I changed the version of BitSeq now it is 1.2.0. But maybe I am misunderstood by the input data files. In the BitSeq manual it is recommended to align data by bowtie and obtain the SAM input file, which I have used TopHat instead of bowtie. Is it necessary to align only with bowtie or I am misunderstood by what you mean about the alignment file.
And then now that I have run my command with this new version I got this error:

(my reference is refseq hg19 the one I have used for the alignment)
res1 <- getExpression("accepted_hits.bam", "genome.fa", log=TRUE,MCMC_burnIn=200, MCMC_samplesN=200, MCMC_samplesSave=50)

## Computing alignment probabilities.
Error in parseAlignment(alignFile, probF, trSeqFile, trInfoFile = trF,  : 
  Main: Transcript info length and sequence length of transcript 0 DO NOT MATCH! (249250621 16571)

Many Thanks in advance.
Best Regards, 
Fatemeh

________________________________________
From: Peter Glaus [glaus at cs.man.ac.uk]
Sent: Tuesday, November 06, 2012 3:19 AM
To: Fatemehsadat Seyednasrollah
Cc: bioconductor at r-project.org
Subject: Re: [BioC] BitSeq input data error

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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