Determining which strain trinity contig belongs to after denovoassembly
Hi all, I have performed a denovo assembly of transcripts obtained from 10 different samples from a species using trinity software. Then, I aligned them with gmap to obtain the trinity contigs which map with the reference genome. Now, at one particular position in the genome, I am observing variants from different trinity contigs. Is there a way to determine which sample the contig belongs to?
Regards,
Sayane
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Align the reads from your samples against the contig. Then you can either visually check the bam files in a browser (IGV etc.) or probe the position with some naive variant calling, e.g samtools mpileup.