Question: Cufflinks Or Alternative From Bwa Alignments?
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gravatar for Biostar User
6.7 years ago by
Biostar User350
Biostar User350 wrote:

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?

cufflinks bwa • 3.1k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 6.7 years ago by Biostar User350
2
gravatar for Mikael Huss
6.7 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

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.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Mikael Huss4.6k

Support this answer!

ADD REPLYlink written 6.7 years ago by yatung180

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.

ADD REPLYlink modified 6.7 years ago • written 6.7 years ago by Geparada1.3k

He specifically mentions isoform assembly of RNA-seq reads, and also writes about starting from aligned SAM/BAM reads.

ADD REPLYlink written 6.7 years ago by Mikael Huss4.6k

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 :)

ADD REPLYlink written 6.7 years ago by Geparada1.3k

True :-) I agree that the original poster needs to get the process clarified.

ADD REPLYlink written 6.7 years ago by Mikael Huss4.6k

I have edited the question now.

ADD REPLYlink written 6.7 years ago by Biostar User350
1
gravatar for Geparada
6.7 years ago by
Geparada1.3k
Cambridge
Geparada1.3k wrote:

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)

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Geparada1.3k
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gravatar for Arun
6.7 years ago by
Arun2.3k
Germany
Arun2.3k wrote:

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.

ADD COMMENTlink written 6.7 years ago by Arun2.3k
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