What is chr EBV in human sam file?
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6.0 years ago
salamandra ▴ 550

I noticed that the header of SAM files resulting from a Bowtie2 besides having the human chromossomes (1-22+x+y+M), also have a EBV chromossome. What is it? Should I be worried?

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SAM Bowtie2 • 3.5k views
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Epstein-Barr-Virus decoy sequence. Plenty of information on that available via a simple google search ;-D

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6.0 years ago
GenoMax 144k

That is Epstein-Barr Virus (human herpes virus genome). Human decoy genome which is what you must have aligned to, has that sequence incorporated in it.

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Don't think so cause these are the names of bowtie2 index files: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.1.bt2 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.2.bt2 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.3.bt2 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.4.bt2 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.rev.1.bt2 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.rev.2.bt2 GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.tar.gz

They have GRCh38, which means they're human. Besides SAM headers have all human chromossomes 1 to 22, X, Y, Mitochondrial, chrUn and then this chr EBV

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Oh i'm sorry, now understand what you mean. It's a decoy, so it's basically normal

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