Understanding transcriptome assembly in newbler
what is the difference between isotig , isogropu and contigs??- For a quick view Isogropus are made of isotigs and isotigs are made of contigs
- Normally one gene should have one transcript, but due to splice variation one gene can have many transcripts. suppose a gene is made of 3 exons, exon 1, exon2 and exon 3. It will generate 3 contigs in newbler, contig 1, contig 2 and contig 3. Due to splice variation the final transcript can be consist of exon1+exon2+exon3 or exon1+exon3 etc.. Thus we get 2 type of variation here, these two are called isotig 1 and isotig 2. isotig 1 consist of contig 1+ contig 2 + contig3 and isotig 2 consists of contig 1+ contig 3. These two isotigs are variation of one transcript. So these 2 isotigs combinedly fall in one isogroup.
- It means that isogroups are transcripts, isotigs are splice variants of one transcript and contigs are separate exons.
- Sometimes primary transcripts can have introns or UTR regions which are also got in form of contigs
- sometimes similar isotigs can be found if come from different sister chromosomes, it can be identified by clustering with cdhit.
Does each exon make up a spearate contig? Can newbler identify exon-exon borders? If the cdna is something like, 1 exon and half of the second exon, then will the whole sequence be considered as one contig/exon?
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