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I am working on trying to finalize a MAGE-TAB format for WGBS. I am basing it
on a standard proposed by Prachi at the DCC. I think we will leave out the VCF
file initially, since it's protected.
Please let me know if you have any suggestions. I would like to submit a
sample version, along with a set of data files (bed6+2) to Anna as soon as
possible. Then we should work on automatically generating it from the same
code as the SRA XML. To avoid duplication, we may want to consider leaving
mapper command line parameters out since they are already in the SRA XML.
Are we currently generating a global "coverage" wig for these (basically the
"raw" findpeaks output)? That seems to be something TCGA analysts would like,
so we should generate it if we are not already. In general, this should be in
all pipelines, not just ChIP-seq.
Original comment by benb...@gmail.com
on 2 Aug 2012 at 1:25
Attachments:
Original comment by benb...@gmail.com
on 16 Aug 2012 at 2:48
sample submission document for TCGA-AA-3518 sent to group for review
Original comment by zack...@gmail.com
on 23 Aug 2012 at 9:55
Please get Bis-SNP info from Yaping and coordinate with Moiz to send to Anna
(cc'ing Prachi since this is based on her proposed sequencing spec).
In general, as many of our pipeline components as possible should log command
line arguments. Maybe wrapper scripts should dump this to stdout where run
scraper can throw them into the QC database?
Original comment by benb...@gmail.com
on 23 Aug 2012 at 10:26
Update:
I've given the COAD submission to prachi for review. There are still details
regarding the official spec that she is working out with SWG. Anna is not
longer with TCGA, so all sequencing submission issues should go to Prachi.
As of now, the ball is out of our court. We will need to wait for them to
finalize the spec (hopefully taking into account our our recommendations) and
get back to us with the final submission procedures.
Original comment by zack...@gmail.com
on 7 Sep 2012 at 12:45
I think maybe we only sent them the MAGETAB file, not the level2 level3 data.
I will send it to Todd Pihl
Original comment by benb...@gmail.com
on 8 Nov 2012 at 10:05
Original comment by zack...@gmail.com
on 12 Feb 2014 at 11:33
submitted all levels
Original comment by zack...@gmail.com
on 23 Jul 2014 at 6:03
Original issue reported on code.google.com by
benb...@gmail.com
on 30 Mar 2011 at 7:55