Assemble RNA-Seq reads

[chengeng]

Hi, everyone

Recently, I wanted to find some software which can assemble the RNA-Seq reads into transcripts. I have tried Velvet and Cufflinks. But because velvet is mainly design to assemble DNA sequencing reads and maybe couldn't correctly assemble RNA-Seq reads. So I used Cufflinks to assemble the RNA-Seq reads finally. But I am confused that why the transcripts in Cufflinks outputs file only contain one start and one end coordinate on the genome? One transcript may contain several exons. Furthermore, Cufflinks can't output the transcript sequences. Can anyone recommend me some sotfware which can assemble RNA-Seq reads? Thanks.


Sincerely,

Geng

[Simon Anders]

Oases: http://www.ebi.ac.uk/~zerbino/oases/

[Siva]

Hi, everyone

Recently, I wanted to find some software which can assemble the RNA-Seq reads into transcripts. I have tried Velvet and Cufflinks. But because velvet is mainly design to assemble DNA sequencing reads and maybe couldn't correctly assemble RNA-Seq reads. So I used Cufflinks to assemble the RNA-Seq reads finally. But I am confused that why the transcripts in Cufflinks outputs file only contain one start and one end coordinate on the genome? One transcript may contain several exons. Furthermore, Cufflinks can't output the transcript sequences. Can anyone recommend me some sotfware which can assemble RNA-Seq reads? Thanks.


Sincerely,

Geng

Geng:
You should try aligning your reads using Tophat (since it also aligns reads spanning splice junctions). You should then use Cufflinks to assemble the Tophat SAM. If you only use bowtie or any other aligner that only maps reads within exons, then Cufflinks will not find any isoforms of transcripts.

hope this helps
Siva
ps: When you deal with mRNA-seq reads you have enriched your sequence for spliced transcripts. So all reads falling within a spliced exon will be 'collapsed' into a transcript. If any one thinks I have got it wrong, please correct me.

[chengeng]

Siva,

Thank you very much for your help. I will try it again.

[chengeng]

Simon Anders,

Thanks. But Oases paper hasn't published, we can't cite it.

[oxydeepu]

Help with assembling RNA-Seq reads.

Hi all.

I dont know is this the thread i should be subscribing. if not sorry. I have a small question. i have ran tophat and cufflinks on RNA-Seq data. I got the output .gtf file. Now i wanted to make a transcript fasta file. I dont know how can i do that.
Please help.
Thank you in advance.

Deepak

[Hobbe]

Hi all.

I dont know is this the thread i should be subscribing. if not sorry. I have a small question. i have ran tophat and cufflinks on RNA-Seq data. I got the output .gtf file. Now i wanted to make a transcript fasta file. I dont know how can i do that.
Please help.
Thank you in advance.

Deepak

Start a new thread please, with this same question. But to get you started, check out Scripture at http://www.broadinstitute.org/software/scripture/home

[oxydeepu]

Hi Robbe..

I dont know how to start a new thread that is why i subscribed this post.
Please suggest me how to..

Thank you
Deepak

[Hobbe]

Go here

http://seqanswers.com/forums/forumdisplay.php?f=18

An then click on New Thread to the left.

[oxydeepu]

Thank you.
I will create a new post.

[jgibbons1]

Simon Anders,

Thanks. But Oases paper hasn't published, we can't cite it.

Oases has been published...

http://bioinformatics.oxfordjournals.org/content/early/2012/02/24/bioinformatics.bts094.short

I use it quite a bit and find it to be very good.

[dpryan]

Oases has been published...

http://bioinformatics.oxfordjournals.org/content/early/2012/02/24/bioinformatics.bts094.short

I use it quite a bit and find it to be very good.

Note the date that the comment you replied to was created and when the paper was submitted

[jgibbons1]

Note the date that the comment you replied to was created and when the paper was submitted

Ahhh...you're right! Whoops...