Q:
In support of an editorial comment I’m working on with a colleague, I just read your paper: The real cost of sequencing: higher than you think!

It is right on the money…as far as the topic I’m interested in but is, obviously, dated (but was helpful for me nonetheless). Pubmed didn’t bring up a more recent revision of your paper…so I assume it hasn’t been updated.

Can you recommend any other, more recent papers or resources that address the issue of cost/price of sequencing? The NHGRI webpage on this topic is also helpful, but it was written in 2016 and does not address the post sequencing costs such as variant calling, annotation, and interpretation. Do you think your illustration of the proportion of costs in 2020 due to the different components of testing still holds true?

A:
see
http://papers.gersteinlab.org/papers/costseq2
http://papers.gersteinlab.org/papers/dsg

Q:
As our University currently doesn’t have access to Cell, I would appreciate if you can send me the pdf file of your recent article in Cell (Kumar et al., issue 5, March 2020).

A:
sure – http://papers.gersteinlab.org/papers/paperE/

Q:
I just read your paper mentioned above. I work in the area of
computational reproducibility so the paper was pretty interesting to
read. However, I stumbled a bit over one of your concluding remarks. You
are saying

"One useful tactic may be detailed sampling: perhaps it is best for the
editor to organize a system wherein, randomly, referees are asked to
review samples in greater detail to ensure the overall quality of the
supplements without quickly overwhelming the peer review system."

I am not sure whether I understood correctly how this could be
implemented. Does it mean that the editor randomly asks one of the
reviewers to look at the supplements, or do all reviewers look at
subsets of supplements? I find this idea pretty interesting and was
wondering whether you have published further articles on this topic?

A:
With respect to: "Does it mean that the editor randomly asks one of the reviewers to look at the supplements, or do all reviewers look at subsets of supplements?"
—> The former

With respect to: "I find this idea pretty interesting and was wondering whether you have published further articles on this topic?"
—> Not exactly.., but you might find useful the related work:
http://papers.gersteinlab.org/papers/structbl
http://papers.gersteinlab.org/papers/SDA

Q:
I’m in need of one of your published articles:

Role of non-coding sequence variants in cancer
https://www.nature.com/articles/nrg.2015.17

I will much appreciate if you could kindly send me a pdf copy of your published article for personal reading.

A:
see http://papers.gersteinlab.org/papers/nrgnccan/index.html

Q:
I saw your paper "Structuring supplemental materials in support of reproducibility" and appreciate your points. I would love to see a forum (like GATK’s forum or StackOverflow) where each topic for a conversation thread is a single published paper. Then everyone who is trying to replicate results could post their questions and authors their answers for all to see. I think this would be much better than the current closed system of emailing the authors. I would love to see a day when a link to a forum is provided on papers, rather than the authors’ email addresses.Who would have the ability to make something like this get started and catch on? Do you know if they are thinking about funding a platform for something like this at the NIH?

A:
with respect to "Who would have the ability to make something like this get started and catch on?"
maybe plos

with respect to "Do you know if they are thinking about funding a platform for something like this at the NIH?"
don’t know

Q:
I have been using the Genboree exceRpt workflow, and loving it! It has saved me so much time! Your paper got me on to it, and I would like to use one of the figures (1) of the exceRpt pipeline in my PhD thesis. Am I right to contact you to request permission? Or should I be heading to Cell for this?

A:
fine w/ me – just acknowledge us (see
https://sites.gersteinlab.org/permissions/)