I have a big genomic file including coordinate as below. 

Data:

    chr10	42383177	42384128
    chr10	42384129	42385080
    chr10	42385081	42386032
    chr10	42386033	42386984
    chr10	42386985	42387936
    chr10	42387937	42388888
    chr10	42388889	42389840
    chr10	42389841	42390793

I would like to extract some features from UCSC like:

- GC content
- conservation score (phastCons)
- repeat fraction (RepeatMasker)

is there any way to download the whole genomic table from UCSC or any script to get those scores for my given coordinates? How can I get those features from UCSC?

Many thanks in advance!
Hello,

These entire data sets are all available from our download server (as well as our API and public mysql for programmatic point access). Here is an example of the data locations for GRCh38/hg38:

* GC content - http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gc5BaseBw.txt.gz
* conservation score (phastCons) - http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/phastConsElements100way.txt.gz
* repeat fraction (RepeatMasker) - http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz

I would also like to mention we have a Data Integrator (http://genome.ucsc.edu/cgi-bin/hgIntegrator) tool. If you upload your bed file, you can then select tracks that it will overlap with your positions and annotate according to those tracks. I made a small bed file with your example positon, chose the following tables for hg38:

* GC Percent
* Conservation - Cons 100 verts
* RepeatMaster

Then configured some of the output fields (to reduce redundancy and simplify the example), and get an output as follows:

<pre>
# hgIntegrator: database=hg38 region=genome Wed Jan 15 09:14:18 2020
#ct_UserTrack_3545.chrom	ct_UserTrack_3545.chromStart	ct_UserTrack_3545.chromEnd	gc5BaseBw.valueAverage	phastCons100way.valueAverage	rmsk.repName	rmsk.repClass	rmsk.repFamily
chr10	42383177	42384128	35.247108		AluSc	SINE	Alu
chr10	42383177	42384128			MER57A-int	LTR	ERV1
chr10	42383177	42384128			LTR19A	LTR	ERV1
chr10	42384129	42385080	47.024185		LTR19A	LTR	ERV1
chr10	42384129	42385080			LTR19-int	LTR	ERV1
chr10	42384129	42385080			AluYi6_4d	SINE	Alu
chr10	42384129	42385080			HERVFH19-int	LTR	ERV1
chr10	42385081	42386032	44.058885		HERVFH19-int	LTR	ERV1
chr10	42385081	42386032			AluSx1	SINE	Alu
chr10	42386033	42386984	44.794953		AluSx1	SINE	Alu
chr10	42386033	42386984			HERVFH19-int	LTR	ERV1
chr10	42386985	42387936	43.238696		HERVFH19-int	LTR	ERV1
chr10	42386985	42387936			AluSg	SINE	Alu
chr10	42386985	42387936			HERVFH19-int	LTR	ERV1
chr10	42387937	42388888	45.467928		HERVFH19-int	LTR	ERV1
chr10	42387937	42388888			AluSx1	SINE	Alu
chr10	42387937	42388888			HERVFH19-int	LTR	ERV1
chr10	42388889	42389840	41.808623		HERVFH19-int	LTR	ERV1
chr10	42389841	42390793	46.491597		HERVFH19-int	LTR	ERV1
chr10	42389841	42390793			AluSz	SINE	Alu
chr10	42389841	42390793			HERVFH19-int	LTR	ERV1
</pre>

You'll notice though that this region does not have conservation scores, looks to be due to repeats. If you have further questions you can email us at genome@soe.ucsc.edu.