Can I use Cufflinks starting from reads in sam/bam format aligned using bwa instead of bowtie? If not, what is the alternative to isoform assembly of RNAseq reads from bwa alignments?
You probably mean Cufflinks rather than TopHat, right? TopHat is a mapper (e. g. FASTQ -> BAM), Cufflinks is a quantifier / assembler (BAM -> FPKM values and/or "transfrags").
You can use BWA-produced SAM/BAM files in Cufflinks, yes.
You will have better result if you just use TopHat 2.0 because this version uses Bowtie 2.0 wich is better than BWA (see this resent published paper)
In theory you can: You could take your fastq and align it using bwa. And from the sam file you could filter out the aligned reads and re-construct a fastq file with the unaligned ones and supply that to tophat. However, as the first stage of mapping, tophat will use bowtie. But I'd guess that there shouldn't be many reads that are mapped using bowtie on unaligned reads.
But then, I also suggest (as Geparada) the approach of using tophat2 and bowtie2, although bowtie2 seems to be in beta version. I am testing this right now.
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Yes, TopHat is a mapper... but uses bowtie to align the seeds to the genome. I think he is looking for a program that uses the same approach than TopHat, but using BWA instead of bowtie.
He specifically mentions isoform assembly of RNA-seq reads, and also writes about starting from aligned SAM/BAM reads.
Yes he did... But maybe he's a little confused about mapping/assembly process. Anyways, one of the two interpretations of the question is right, and either your answer or mine will help him :)
True :-) I agree that the original poster needs to get the process clarified.
I have edited the question now.