Open nservant opened 6 years ago
Those are to be found experimentally. I do not know them :/ But the original SICER README.pdf contained some suggestions.
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 :)
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
But a generic name/description like that is not particularly helpful, methinks.
On Mon, Jul 9, 2018 at 6:11 PM Nicolas Servant notifications@github.com 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
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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 ....
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 :)
On Tue, Jul 10, 2018 at 9:58 AM Nicolas Servant notifications@github.com 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 ....
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Perfect ! Thanks
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.
On Tue, Jul 10, 2018 at 10:43 AM Nicolas Servant notifications@github.com wrote:
Perfect ! Thanks
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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
Hi, Thanks for developing epic which is much more stable than SICER ! that's great. I have two comments: