what could be the possible reason of getting multiple contigs with same annotation in transcriptome analysis. If we are getting no. of contigs showing same annotation then how to select the contigs among them, for downstream analysis.Whether certain sorts of Statistical analysis are to be performed for that, If so then what type of statistical approaches we can use for study.
As Mikael says you can have different isoforms of the same gene assembled into multiple contigs. In cases of alternative splicing you might get multiple transcripts that have a high percentage of overlap and only differ where an intron was retained in one transcript and not the other, or an alternative 5' or 3' splice site was used resulting in just a few nucleotides difference. I often see this in transcript assemblies. Depending on your downstream analysis you may want to select just the longest isoform for each gene, or to avoid introns in your sequence you could select the shortest ones. This could be accomplished with a simple script.
You can have different isoforms of the same gene or your assembly is fragmented. Your contig is simply different parts of the same gene. There are attempts to solve this with a clustering step. Have a look at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4165373/
As Mikael says you can have different isoforms of the same gene assembled into multiple contigs. In cases of alternative splicing you might get multiple transcripts that have a high percentage of overlap and only differ where an intron was retained in one transcript and not the other, or an alternative 5' or 3' splice site was used resulting in just a few nucleotides difference. I often see this in transcript assemblies. Depending on your downstream analysis you may want to select just the longest isoform for each gene, or to avoid introns in your sequence you could select the shortest ones. This could be accomplished with a simple script.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics