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Old 10-20-2015, 01:56 AM   #45
Alicia B
Location: Aberdeen

Join Date: Sep 2015
Posts: 10

Originally Posted by clarissaboschi View Post
Dear members,

I am using data from Illumina next generation sequencing from different chickens. I have different bam files (for each chicken), and I obtained the test.hits using the command line:
samtools view –F 4 file1.bam | perl –lane ‘print “$F[2]\t$F[3]”’ > test1.hits

But I need to have also the ref.hits, but I only have the reference chicken genome reference (fasta file). How can I get this ref.hits?

@clarissaboschi did you ever find a solution to your question regarding what to use as a a ref-hits file? I am in what seems to be a similar situation to yours: I don't have a control sample and I am only trying to detect CNVs in various individuals (rice) comparing it to the reference genome. What did you end up doing?

Thanks for your help!
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