trackline and recommanded parameters

[nservant]

Hi,
Thanks for developing epic which is much more stable than SICER ! that's great.
I have two comments:

• If I'm correct, the output bed files are generated for UCSC visualization. Adding a trackline would be great in that case.
• I think that other users already ask it, but having recommended parameters for different histone mark would be extremely useful.
  I guess --window-size, --gaps-allowed and --false-discovery-rate-cutoff can be updated.
  Any advice is welcome !

[endrebak]

Those are to be found experimentally. I do not know them :/ But the original SICER README.pdf contained some suggestions.

[endrebak]

Output bed files are also created for downstream analysis in bedtools etc.

I could add a track line, but I do not know what I'd put there :)

[nservant]

i would suggest to add a parameter "--trackline", that simply add something a header like
"track name=pairedReads description="Clone Paired Reads" useScore=1"
See https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for details
Thanks

[endrebak]

But a generic name/description like that is not particularly helpful, methinks.

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On Mon, Jul 9, 2018 at 6:11 PM Nicolas Servant ***@***.***> wrote: i would suggest to add a parameter "--trackline", that simply add something a header like "track name=pairedReads description="Clone Paired Reads" useScore=1" See https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for details Thanks — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#81 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQ9I0hRn4cHlMESqQDqSQKSQXtizfSg2ks5uE4C1gaJpZM4VFto8> .

[nservant]

Sure. You can have a look at the Macs2 documentation for example.
It takes a --name option, and thus is the name in the "name=" and "description=" field.
Another idea would be to simply use the basename of the input file ....

[endrebak]

There can be multiple input files so the basename cannot be used in general. I'm trying to cut down on features atm and instead outsource them to other packages. But I will think about it/see if there are more requests for this. Keeping the issue open :)

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On Tue, Jul 10, 2018 at 9:58 AM Nicolas Servant ***@***.***> wrote: Sure. You can have a look at the Macs2 documentation for example. It takes a --name option, and thus is the name in the "name=" and "description=" field. Another idea would be to simply use the basename of the input file .... — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#81 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQ9I0kgemWhvMHGjEoc9vDJ1gTZFrgyNks5uFF6LgaJpZM4VFto8> .

[nservant]

Perfect ! Thanks

[endrebak]

Do not use UCSC much, but aren't there tracklines in bigwigs? That would also probably be a nice thing to add, since modifying binary formats is much harder.

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On Tue, Jul 10, 2018 at 10:43 AM Nicolas Servant ***@***.***> wrote: Perfect ! Thanks — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#81 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQ9I0tY5dVFLvt8c4Eg5yxiALux7vDLNks5uFGkxgaJpZM4VFto8> .

[nservant]

For the bigwig, I think that the user can add its trackline when the data are loaded ;
track type=bigWig name="My Big Wig" description="A Graph of Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigWig.bw