RepeatMasker Table Output

[John Allan Morris]

Hello,

From the Table Browser page I am trying to generate a list of all the elements masked by RepeatMasker for approximately 400 sequences that I've uploaded.  The output as BED files only contains the name of the specific repeat, but I was wondering if I could get output like in the Sample Rows example?  It lists the repeat families and repeat classes.

I've posted the sample rows given at the bottom.  Unfortunately, my output is not as comprehensive as this.  How do I make it look like this table?

Thanks,

John

bin	swScore	milliDiv	milliDel	milliIns	genoName	genoStart	genoEnd	genoLeft	strand	repName	repClass	repFamily	repStart	repEnd	repLeft	id
607	687	174	0	0	chr1	3000001	3000156	-194195276	-	L1_Mur2	LINE	L1	-4310	1567	1413	1
607	917	214	114	45	chr1	3000237	3000733	-194194699	-	L1_Mur2	LINE	L1	-4488	1389	913	1
607	215	31	0	30	chr1	3000733	3000766	-194194666	+	(TTTG)n	Simple_repeat	Simple_repeat	2	33	0	2
607	845	233	76	114	chr1	3000766	3000792	-194194640	-	L1_Mur2	LINE	L1	-6816	912	887	1
607	621	250	65	37	chr1	3001287	3001583	-194193849	-	Lx9	LINE	L1	-1596	6048	5742	3
607	1320	197	332	7	chr1	3001722	3002005	-194193427	-	RLTR25A	LTR	ERVK	0	1028	625	4
607	414	0	0	0	chr1	3002005	3002051	-194193381	+	(TA)n	Simple_repeat	Simple_repeat	1	46	0	5
607	2352	193	69	64	chr1	3002051	3002615	-194192817	-	RLTR25A	LTR	ERVK	-404	624	1	4
607	386	268	145	138	chr1	3003212	3003261	-194192171	-	L1M2	LINE	L1	-1343	4800	4769	6
607	797	201	147	0	chr1	3003261	3003445	-194191987	-	B3	SINE	B2	-2	214	4	7

[Brooke Rhead]

Hi John,

If you select the "all fields from selected table" as the output format,
you will get rows that look like your sample rows. However, if you have
intersected the RepeatMasker track with a custom track (so that you can
limit the output), you won't see the "all fields" option. To get around
this problem, instead of intersecting the table with a custom track, you
can use the "defined regions" function, which will let you enter up to
1,000 rows in BED format. Using "defined regions" instead of a custom
track will still let you limit output to your desired regions in the
Table Browser, and it will give you the option to select "all fields" as
the output format.

I hope this answer solves your problem. If you have further questions,
please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

> --
>
>
>

[John Allan Morris]

Hello,

I've tried to follow the instructions and I originally did have a "defined region" uploaded of about 400 rows in BED format.  I'm still not seeing an "all fields from selected table" option under output format.  All I see is "sequence", "GTF - gene transfer format", "BED - browser extensible data", "custom track", and "hyperlinks to Genome Browser".

I don't believe I've intersected the RepeatMasker track with a custom track.  I've removed any custom tracks that I had.  Under group I have "Variation and Repeats" and under track I have "RepeatMasker".

I'm using the July 2007 build of the mouse genome, if this matters.

Thanks for all the help,

John

[Brooke Rhead]

Hi John,

I should have said if you have created an intersection of RepeatMasker
with any track (not just a custom track), you will not see the "all
fields from selected table" output option. If there is an intersection,
you should see a line in the Table Browser that says "intersection with
(whatever table): edit clear", along with a note just above the get
output button that says "Note: The all fields and selected fields output
formats are not available when an intersection has been specified."

If you don't see the indicators that an intersection has been done, and
you still don't see the "all fields" output option, you can try
resetting your cart. To do so, click the link just below the get output
button that says "To reset all user cart settings (including custom
tracks), click here." (Note that this will cause any settings you may
have made in the Genome Browser, including defined regions and custom
tracks, if any remain, to be lost.)

If that still doesn't solve the problem, please write back, and we can
help troubleshoot further.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 3/15/13 2:55 PM, John Allan Morris wrote:
> Hello,
>

> I've tried to follow the instructions and I originally did have a
> "defined region" uploaded of about 400 rows in BED format. I'm still
> not seeing an "all fields from selected table" option under output
> format. All I see is "sequence", "GTF - gene transfer format", "BED -
> browser extensible data", "custom track", and "hyperlinks to Genome
> Browser".
>
> I don't believe I've intersected the RepeatMasker track with a custom
> track. I've removed any custom tracks that I had. Under group I have
> "Variation and Repeats" and under track I have "RepeatMasker".
>
> I'm using the July 2007 build of the mouse genome, if this matters.
>
> Thanks for all the help,
> John
>

> --
>
>
>