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Old 02-20-2013, 11:25 AM   #1
yzzhang
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Default use RNA-seq to improve genome assembly

Dear all,
Now I am assembling a plant genome using illumina 2*100 DNA and RNA-seq paired end reads. Because I have just one insert size library, so I got so many denovo assembled contigs using DNA reads , I wanted to improve the assembly using RNA-seq data, I just know that RNAPATH can do this from one genome research pepar publised on 2010.

I followed the manual of erange, first I mapped my RNA reads to my draft assembly using bowtie, then blat the unmapped reads to draft assembly, now I got the blat results for reads 1 and reads 2. Then I need to run makerdsfromblat.py and distalPairs.py. Because distalPairs.py is used for to find the paired end reads that do not map to the same contig and seems just accept one input file, so I wonder how my reads1 and reads 2 file are feed to
distalPairs.py? Does anyone know it ?
Or other software can improve scaffolding using RNA-seq?
I appriacte your answer, Thanks very much.
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Old 02-20-2013, 12:29 PM   #2
colindaven
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You could try SSPACE too, it automates the process a lot more.
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Old 02-20-2013, 01:00 PM   #3
yzzhang
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Thanks for your suggestion. But I am wondering if I can feed sspace with RNA-seq reads? for RNA-seq, the reads contain many splice. How to do this? I read the sspace manual, there is no mention about RNA. Please help. Thanks a lot!
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Originally Posted by colindaven View Post
You could try SSPACE too, it automates the process a lot more.
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Old 11-20-2013, 11:57 PM   #4
elzed
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I am wondering if you have work out the way to incoporate RNAseq reads into genome assembly.

I am interested in it.

Cheers

elzed
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Old 11-21-2013, 04:15 AM   #5
yzzhang
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Hi,
No, I gave up finally after trying RNAPATH and SSPACE, if you have good news about it, please let me know.
Best,
yz
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Originally Posted by elzed View Post
I am wondering if you have work out the way to incoporate RNAseq reads into genome assembly.

I am interested in it.

Cheers

elzed
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Old 11-26-2013, 11:14 PM   #6
colindaven
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This might be interesting, but I haven't tried it. It seems to require long reads.

Xue, W.; Li, J.-T.; Zhu, Y.-P.; Hou, G.-Y.; Kong, X.-F.; Kuang, Y.-Y. & Sun, X.-W. L_RNA_scaffolder: scaffolding genomes with transcripts. BMC Genomics, 2013, 14, 604 Abstract: Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments.We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased.The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.
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