Hi Katrina,
Thanks for your response.
actually i have read that mail before i post again to this list.
I didnot find a solution in that link....
also in the download page
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/
is says:chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
RepeatMasker was run with the -s (sensitive) setting.
Using: Jan 29 2009 (open-3-2-7) version of RepeatMasker and
RELEASE 20090120 of library RepeatMaskerLib.embl
i found in this link http://www.girinst.org/server/archive/RepBase14.01/
do have a
repeatmaskerlibraries-20090120.tar.gz<http://www.girinst.org/server/archive/RepBase14.01/protected/repeatmaskerlibraries/repeatmaskerlibraries-20090120.tar.gz>
after download and extraction, i didnot found a L1MC name in the
library file, this really confused me
$ grep 'L1MC' Libraries/RepeatMaskerLib.embl
ID L1MC1_3end repeatmasker; DNA; ???; 1080 BP.
CC L1MC1_3end DNA
DE RepbaseID: L1MC1
ID L1MC2_3end repeatmasker; DNA; ???; 1091 BP.
CC L1MC2_3end DNA
DE RepbaseID: L1MC2
ID L1MC3_3end repeatmasker; DNA; ???; 2532 BP.
CC L1MC3_3end DNA
DE RepbaseID: L1MC3
ID L1MC4_3end repeatmasker; DNA; ???; 2789 BP.
CC L1MC4_3end DNA
DE RepbaseID: L1MC4
ID L1MC4_3endX repeatmasker; DNA; ???; 2789 BP.
CC L1MC4_3endX DNA
ID L1MC4_5end repeatmasker; DNA; ???; 2555 BP.
CC L1MC4_5end DNA
DE RepbaseID: L1MC4_5end
ID L1MC4a_3end repeatmasker; DNA; ???; 2629 BP.
CC L1MC4a_3end DNA
ID L1MC5_3end repeatmasker; DNA; ???; 1351 BP.
CC L1MC5_3end DNA
DE RepbaseID: L1MC5
ID L1MC_orf2 repeatmasker; DNA; ???; 3294 BP.
CC L1MC_orf2 DNA
CC Description: L1MC1 consensus
ID L1MCa_5end repeatmasker; DNA; ???; 2434 BP.
CC L1MCa_5end DNA
DE RepbaseID: L1MCA_5
ID L1MCb_5end repeatmasker; DNA; ???; 1197 BP.
CC L1MCb_5end DNA
DE RepbaseID: L1MCB_5
ID L1MCc_5end repeatmasker; DNA; ???; 1536 BP.
CC L1MCc_5end DNA
DE RepbaseID: L1MCC_5
CC encoding a gag protein 72% similar to L1MC4_gag
CC (80%) to L1MC4_5end from 846 to 2237 (end)
look forward to your further response if you have.
Thank you so much.
On Fri, Sep 16, 2011 at 2:02 PM, Katrina Learned <[email protected]>wrote:
> Hi Daofeng,
>
> Please see this previously answered mailing list question:
> https://lists.soe.ucsc.edu/**pipermail/genome/2011-January/**024826.html<https://lists.soe.ucsc.edu/pipermail/genome/2011-January/024826.html>
>
> Please contact the mail list ([email protected]) again if you have any
> further questions.
>
> Katrina Learned
> UCSC Genome Bioinformatics Group
>
>
> On 9/16/11 9:40 AM, Daofeng Li wrote:
>
>> Dear UCSC Genome Browser admins,
>>
>> Was the repeat consensus sequence for hg19 available for download?
>> as i saw in
>> http://genome.ucsc.edu/cgi-**bin/hgTables?db=hg19&hgta_**
>> group=varRep&hgta_track=rmsk&**hgta_table=rmsk&hgta_doSchema=**
>> describe+table+schema<http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=rmsk&hgta_table=rmsk&hgta_doSchema=describe+table+schema>
>> there was a repName called L1MC, but i didnot find its sequence it
>> downloaded Repbase fasta files
>>
>> i also noticed that "UCSC has used the most current versions of the
>> RepeatMasker software and repeat libraries available to generate these
>> data.
>> Note that these versions may be newer than those that are publicly
>> available
>> on the Internet.
>> "
>> So might be these difference caused my problem. Is there any place for
>> download or could you provide me with this file？
>>
>> Thanks for your help
>>
>> Best wishes.
>>
>>
--
Daofeng
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