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Old 10-01-2014, 08:03 AM   #1
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Location: Ann Arbor

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Default Cufflinks hg19 vs hg19_Broad_variant

I am trying to use Cufflinks (Cuffquant and Cuffnorm) to generate gene/transcript expression levels from the CCLE RNAseq data on cghub. The RNAseq data is provided as bam files aligned to genome assembly hg19_Broad_variant. The transcriptome assembly I would like to use is based on hg19/GRCh37. I have not found much information on hg19_Broad_variant to understand how different it is from hg19/GRCh37.

Do I need to convert the CCLE bam files to hg19/GRCh37 before putting them through a Cufflinks workflow? Or is hg19_Broad_variant close enough that it will work without conversion?

If I have to convert to hg19/GRCh37, is it possible to liftOver bam files? Or do I have to do bam->fastq using hg19_Broad_variant, then start over with alignment to hg19/GRCh37?

Thanks in advance for any advice.
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Old 10-02-2014, 12:19 PM   #2
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Default HG19_Broad_variant

This is the explanation I received from the Broad:

The file is essentially what UCSC uses for the HG19 primary assembly plus EBV.

All the files we submit have a sequence dictionary that clearly gives
the accession numbers for all of the sequences. In addition it
contains a URL to the broad's public FTP site for the fasta file.
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Old 01-26-2016, 09:29 AM   #3
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So I guess that the gene coordinates do not change between UCSC hg19 and hg19_broad. Am I right?
Thanks a lot!
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broad_variant cufflinks

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