HeLa reference fasta

Question

[Sergio Martínez Cuesta]

Dear all,

My first question is if there is / where to find a referece .fasta file for the HeLa cell line.

I am working with several DNA sequencing samples from HeLa. So far I have used UCSC's hg19 as a reference, however when aligning with bwa I can see a lot of R1 fwd alignments with a lot of soft clipping at the 5' in my particular regions of interest. I am starting to think whether this might be due to structural variation differences between hg19 and HeLa beginning around where I am looking into.

My second question is on how to generate a customised reference fasta file from a standard reference fasta file and variation data. Any publication/software describing how to do this?

There are several 2013 efforts studying variation in HeLa. I thought that perhaps combining hg19 with single nucleotide and structural variations files might do what I need.

Any ideas?

[karl.stamm]

According to the most comprehensive review of the HeLa genome I've seen, it's not a small change between it and hg19. It's a completely rearranged cell line. https://www.ncbi.nlm.nih.gov/pubmed/23550136

Answer 1

[GenoMax]

I believe that you need to apply for access to HeLa cell data. More information here.

[Jean-Karim Heriche]

Yes, you need to request access to the data from dbGAP. From what I've been told, requesting access is a pain and has to be done for each use of the data separately plus access authorization expires quickly and has to be renewed. My opinion is that if the HeLa genome sequence is of long term interest to several projects in your lab, you'd be better off sequencing the HeLa cells you're using. Code from the Landry et al. paper should be freely available.