Hello Challengers - A lexicographically-sorted submission template bedGraph has been added to the Files:/data/submission_template/ folder [here](https://www.synapse.org/#!Synapse:syn18145317). The UCSC bedGraphToBigWig utility is easier to use with that sort order than with the numerical sort order we first supplied.
The submission format requirements are clarified in [Section 3.4 of the wiki](https://www.synapse.org/#!Synapse:syn17083203/wiki/588658).
Good luck!
Seth
Created by J Seth Strattan jseth @cying for simplicity and consistency we don't remove the blacklisted regions from the bigWigs, we just ignore the values there for scoring purposes. So, yes, as you say, those regions could have any value.
Seth
Hello Seth,
I have a question for the blacklist part.
In the Wiki is mentioned, 'Intervals overlapping blacklisted regions in the genome (showing strange artifacts of signal due to repeats) will be ignored for scoring performance.'
But for the submission_template. which the length of it is included blacklisted regions.
So finally, what we handle should include the blacklist regions or without it?
If with it, the number of those part could be any value? Thanks for the reply! @YSun.55 you are correct, chrY is excluded from this challenge.
Seth
Hello Seth,
I just found that the 'submission_template.bigwig' file in folder 'Files:/data/submission_template/' does not include chrY. Here is the output from bigWigInfo:
version: 4
isCompressed: yes
isSwapped: 0
primaryDataSize: 317,356,923
primaryIndexSize: 3,812,320
zoomLevels: 10
chromCount: 23
basesCovered: 3,031,042,417
mean: 0.000000
min: 0.000000
max: 0.000000
std: 0.000000
Does that mean we are not required to impute for chromosome Y ?
Thanks a lot.
Steven @ccchang0111 thanks for your question, Andrew. Yes you can (and should) just submit in bigwig format. And, yes, the submission_template.bigwig is in the correct format, so you can just replace the values in that file. The bedgraph files are just a convenience if you want to have a text-based format that is easily convertible to bigwig. But if you don't need it, then you can ignore the bedgraph.
Seth
Hello Seth,
Can we just use "submission_template.bigwig", replace those zeros with our predicted values, and then submit that bigwig file? Will it give me the right format for submission?
I am not familiar with bedgraph, so I am a bit confused about why there are bedgraph and bigwig files in the "submission_template" folder?
Accessing bigwig file is much faster than bedgraph, therefore it will be nice if I can ignore those bedgraph files.
Thank you so much!
Andrew