[khmer] Fwd: About Khmer and Trinity.

[C. Titus Brown]

On Thu, Jan 16, 2014 at 07:01:49PM +0000, Won C Yim wrote:
> 
> Dear Brown,
> 
> Hi!
> 
> I have question.

;) Let's see if we can help. First, some clarifications:

> I have a 114 reads data.

114m reads?

> First I ran Trinity with whole dataset with adapter and quality trimmed fastq.
> 
> The no. of contigs were 108,112 .
> 
> After your normalization it generated 22,454 contigs.
> 
> I know it works well but our species has 295Mb.
> 
> The Ararbidopsis is 135Mb and have 30,000 genes.
> 
> I think 22,454 contigs were to small.
> 
> Do I lost something?

My main question is, what exactly did you run for normalization?  We have
a protocol here:

https://khmer-protocols.readthedocs.org/en/v0.8.4/mrnaseq/

that has worked fairly well in the past.

best,
--titus

> > Dear Brown,
> > 
> > Hi!
> > 
> > I have question.
> > 
> > I have a 114 reads data.
> > 
> > First I ran Trinity with whole dataset with adapter and quality trimmed fastq.
> > 
> > The no. of contigs were 108,112 .
> > 
> > After your normalization it generated 22,454 contigs.
> > 
> > I know it works well but our species has 295Mb.
> > 
> > The Ararbidopsis is 135Mb and have 30,000 genes.
> > 
> > I think 22,454 contigs were to small.
> > 
> > Do I lost something?
> > 
> > Please help.
> > 
> > Thank you.
> > 
> > Won
> > __
> > Yim, Won Cheol
> > 
> > Postdoctoral Fellow
> > 
> > MS330/Department of Biochemistry & Molecular Biology
> > 1664 N. Virginia Street
> > University of Nevada
> > Reno, NV 89557-0330
> > 
> > Mobile:775-229-0453
> > Email: wcyim at unr.edu
> > http://ascendo.u.googlepages.com
> > 
> > Jan 10, 2014, 5:29 AM, C. Titus Brown <ctb at msu.edu> ????:
> > 
> >> Hi Won, the k-mer size is not directly analogous.  We've had fine experience
> >> with k=20.
> >> 
> >> best,
> >> --titus
> >> 
> >> On Fri, Jan 10, 2014 at 06:19:21AM +0000, Won C Yim wrote:
> >>> Dear Titus,
> >>> 
> >>> Hi!
> >>> 
> >>> I have a question for your tutorial.
> >>> 
> >>> I think Trinity use 25mer for assembly.
> >>> 
> >>> Is it Okay to use 20mer for kmer?
> >>> 
> >>> Thank you.
> >>> 
> >>> Won
> >>> __
> >>> Yim, Won Cheol
> >>> 
> >>> Postdoctoral Fellow
> >>> 
> >>> MS330/Department of Biochemistry & Molecular Biology
> >>> 1664 N. Virginia Street
> >>> University of Nevada
> >>> Reno, NV 89557-0330
> >>> 
> >>> Mobile:775-229-0453
> >>> Email: wcyim at unr.edu<mailto:wcyim at unr.edu>
> >>> http://ascendo.u.googlepages.com
> >>> 
> >>> 2013. 12. 18., ???? 10:45, C. Titus Brown <ctb at msu.edu<mailto:ctb at msu.edu>> ????:
> >>> 
> >>> Hi Won,
> >>> 
> >>> https://khmer-protocols.readthedocs.org/en/v0.8.4
> >>> 
> >>> best,
> >>> --titus
> >>> 
> >>> On Wed, Dec 18, 2013 at 06:38:18PM +0000, Won C Yim wrote:
> >>> Dear Titus Brown,
> >>> 
> >>> Hi !
> >>> 
> >>> I am Won Cheol Yim in University of Nevada, Reno.
> >>> 
> >>> Recently, I try to de novo assemble one of plant species (~350Mb) by using RNA-seq data.
> >>> 
> >>> I already assembled by Trinity alone and Trinity normalization program.
> >>> 
> >>> But the result is too bad.
> >>> 
> >>> Actually we have deep sequencing (250GB of 100bp Illumina single read).
> >>> 
> >>> So there is so many weird contigs.
> >>> 
> >>> I read many things about that like cut-off based on FPKM and Isoform percent.
> >>> 
> >>> However there??s no answer.
> >>> 
> >>> I think Khmer can help my dataset.
> >>> 
> >>> Is it possible to use Khmer with Trinity.
> >>> 
> >>> There is no reference paper.
> >>> 
> >>> And Trinity use 25 kmer as default.
> >>> 
> >>> Can you advice me the critical options?
> >>> 
> >>> I??ve used ?? normalize-by-median.py -k 20 -C 20 --hashsize 2e9 --n_hashes 4 all.fastq  ??
> >>> 
> >>> My fastq file is already trimmed by Q>20 and illumina adaptors.
> >>> 
> >>> Would you mind advice me some helpful comment?
> >>> 
> >>> Thank you.
> >>> 
> >>> Won
> >>> 
> >>> 
> >>> 
> >>> __
> >>> Yim, Won Cheol
> >>> 
> >>> Postdoctoral Fellow
> >>> 
> >>> MS330/Department of Biochemistry & Molecular Biology
> >>> 1664 N. Virginia Street
> >>> University of Nevada
> >>> Reno, NV 89557-0330
> >>> 
> >>> Mobile:775-229-0453
> >>> Email: wcyim at unr.edu
> >>> http://ascendo.u.googlepages.com
> >>> 
> >>> 
> >>> --
> >>> C. Titus Brown, ctb at msu.edu
> >>> 
> >> 
> >> -- 
> >> C. Titus Brown, ctb at msu.edu
> > 
> 
> _______________________________________________
> khmer mailing list
> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer

-- 
C. Titus Brown, ctb at msu.edu