BitSeq

narges · 11-05-2012, 06:04 AM

Hi,
I wanted to know what kind of input data I can use running BitSeq. I have the fastq files of the experiment plus the accepted hits bam file from TopHat. Are these files the acceptable input files for "getExpression" function in BitSeq and if so, associated to each bam file from Tophat I have several fastq files which are the technical replicates of that sample. Should I use all the technical fastq files when running the "getExpression" function separating with comma?

Many thanks in advance.

peto · 11-19-2012, 02:53 PM

Hi,
probably a very late answer for you, but just in case someone else stumbles across the same issue.

TopHat is designed for spliced alignment of reads against genomic sequence. BitSeq, on the other hand, is designed for use with reads aligned to transcriptomic sequence. The input reference Fasta has to be assembled transcriptome sequence* and reads should be aligned with some aligner that allows multiple alignments (e.g. Bowtie).

If you have other questions or want more information about BitSeq, it might be faster to contact us directly through official channels at Bioconductor or google code.

Regards,
Peter.

* transcriptome reference can be either acquired from ensembl or UCSC table browser

11-05-2012, 06:04 AM	#1
narges Member Location: Finland Join Date: Aug 2012 Posts: 29	BitSeq input data Hi, I wanted to know what kind of input data I can use running BitSeq. I have the fastq files of the experiment plus the accepted hits bam file from TopHat. Are these files the acceptable input files for "getExpression" function in BitSeq and if so, associated to each bam file from Tophat I have several fastq files which are the technical replicates of that sample. Should I use all the technical fastq files when running the "getExpression" function separating with comma? Many thanks in advance. Last edited by narges; 11-05-2012 at 07:05 AM.

11-19-2012, 02:53 PM	#2
peto Junior Member Location: UK Join Date: Nov 2012 Posts: 1	Hi, probably a very late answer for you, but just in case someone else stumbles across the same issue. TopHat is designed for spliced alignment of reads against genomic sequence. BitSeq, on the other hand, is designed for use with reads aligned to transcriptomic sequence. The input reference Fasta has to be assembled transcriptome sequence* and reads should be aligned with some aligner that allows multiple alignments (e.g. Bowtie). If you have other questions or want more information about BitSeq, it might be faster to contact us directly through official channels at Bioconductor or google code. Regards, Peter. * transcriptome reference can be either acquired from ensembl or UCSC table browser