Question: whole genome fasta/gtf for cell lines
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gravatar for marongiu.luigi
3.6 years ago by
Germany, Mannheim, UMM
marongiu.luigi420 wrote:

Hello,
I need to create a reference sequence index for TopHat; it is straightforward for the human chromosomes alone, but what if I need to index genomes from human cell lines containing viral integrated sequences, for instance SiHa (containing human papillomavirus) and Akata (containing Epstein-Barr virus)? How can a create a reference for these cells? Is there a GTF file for cell lines?
Thank you,
L.

rna-seq assembly genome • 1.2k views
ADD COMMENTlink modified 3.6 years ago by michael.ante3.5k • written 3.6 years ago by marongiu.luigi420
0
gravatar for michael.ante
3.6 years ago by
michael.ante3.5k
Austria/Vienna
michael.ante3.5k wrote:

Hi Luigi,

You can either create a combined index by combining the fasta files and the gtfs of human and the virus annotation, or create an index for the virus genomes and map to that first. The unmapped reads can then be used to align against the human annotation.

Cheers

Michael

ADD COMMENTlink written 3.6 years ago by michael.ante3.5k
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