Question: Custom reference genome for hybride mouse
0
gravatar for ddjima2014
16 days ago by
ddjima20140
ddjima20140 wrote:

I haven’t worked with hybrid genome before, I am trying to create a custom genome to align RNA-Seq that was generated from hybrid mouse. Would you please guide me how to create a custom genome for two hybrid mouse? The strains are C57BL and 6NJ. I have aligned to the mouse reference genome (C57BL) and the unique aligned reads percentage is around 65%, this is not good from my experience.

rna-seq • 88 views
ADD COMMENTlink modified 16 days ago by Shalu Jhanwar400 • written 16 days ago by ddjima20140
1

Would you please guide me how to create a custom genome for two hybrid mouse?

What exactly are you trying to do here? Is this a hybrid of two known parents (C57BL and 6NJ) ?

Have you checked a few reads that do not map to make sure they are still mouse and not some contamination.

ADD REPLYlink modified 16 days ago • written 16 days ago by genomax87k

I have aligned to the mouse reference genome (C57BL) and the unique aligned reads percentage is around 65%

For RNA-seq, 65% aligned reads is actually within the normal range. That fraction can change substantially depending on the sample prep, such as RNA quality and library kit.

Different strains should not be that different.

ADD REPLYlink written 16 days ago by igor11k
0
gravatar for Shalu Jhanwar
16 days ago by
Shalu Jhanwar400
Switzerland
Shalu Jhanwar400 wrote:

You can directly download the FASTA sequences from C57BL_6NJ_v1 assembly for Mus musculus from here under "Chromosome" tab. After downloading, you can concatenate all the FASTA files into one to generate a reference fasta for alignment of RNA-seq reads. You can use below code for creating single reference fasta:

cat fasta_file1 fasta_file2 fasta_filen > reference fasta
ADD COMMENTlink modified 16 days ago • written 16 days ago by Shalu Jhanwar400
1

While this would create a hybrid genome it would be a simple compilation of two haploid genomes that are still separate so there would be a large amount of duplication of sequences, which will cause issues with almost all reads multi-mapping. If @ssjima2014 is looking at a hybrid of those two parental strains then the hybrid genome will be recombinant of the two parents, so alternating parts will be identical to parental genomes.

Note: It is not clear to me if a genome assembly is available for C57BL_6NJ_v1 hybrid directly at EBI.

ADD REPLYlink modified 16 days ago • written 16 days ago by genomax87k
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