I was hoping people would help me understand a weird situation I have encountered.
I have a genome assembly of a fungal genome (not done by me) which I have mapped raw RNAseq reads onto. RNAseq generally agrees quite well with predicted genes.
However in one gene that we are working on, the RNAseq agrees with the gene calls, but unlike other "genes" right next door on the same scaffold, all of the mapped reads are from one end of the paired end reads. The gene is big enough so that if one paired end read maps onto one end of the gene, the other one should logically be at the other end of the gene, which is the case in other genes next door.
Additionally, this weird gene has an identical copy right next door (this may be an assembly artefact)
Anyone have any idea what could cause this?
Genome assembled using velvet (I think.. not done by me) from multiple paired-end and mate-pair illumina runs.. transcriptome also from illumina runs.
I have a genome assembly of a fungal genome (not done by me) which I have mapped raw RNAseq reads onto. RNAseq generally agrees quite well with predicted genes.
However in one gene that we are working on, the RNAseq agrees with the gene calls, but unlike other "genes" right next door on the same scaffold, all of the mapped reads are from one end of the paired end reads. The gene is big enough so that if one paired end read maps onto one end of the gene, the other one should logically be at the other end of the gene, which is the case in other genes next door.
Additionally, this weird gene has an identical copy right next door (this may be an assembly artefact)
Anyone have any idea what could cause this?
Genome assembled using velvet (I think.. not done by me) from multiple paired-end and mate-pair illumina runs.. transcriptome also from illumina runs.
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