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jyhehir / mobster

For more details about Mobster please see
https://jyhehir.github.io/mobster/index.html
GNU General Public License v3.0
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How to make REPEATMASK_FILE? #33

Closed npaulat closed 4 years ago

npaulat commented 5 years ago

Hello,

I am trying to run Mobster on my own data, and I would like to know what the required format of the REPEATMASK_FILE in the Mobster.properties? I looked at the example ../resources/repmask/hg19_alul1svaerv.rpmsk file, and I am unfamiliar with the format and the file extension, as it looks similar to, but not the same as a RepeatMasker .fa.out file. Could you please clarify? If this is an older output format from RepeatMasker, will Mobster accept the newer format, or how should this file be made?

Thank you, Nikki

jyhehir commented 5 years ago

Dear Nikki, Thanks for trying Mobster. Indeed I have not updated the repeatmask files recently.These can be directly downloaded from the UCSC. via the table browser https://genome.ucsc.edu/cgi-bin/hgTables select the genome buildgroup = repeatsthen add a custom filter repFamily = 'Alu' OR repFamily = 'L1' OR repName like 'HERV%' OR repFamily = 'SVA'

Regards,Jayne On Wednesday, 6 November 2019, 12:39:54 am GMT+1, npaulat notifications@github.com wrote:

Hello,

I am trying to run Mobster on my own data, and I would like to know what the required format of the REPEATMASK_FILE in the Mobster.properties? I looked at the example ../resources/repmask/hg19_alul1svaerv.rpmsk file, and I am unfamiliar with the format and the file extension, as it looks similar to, but not the same as a RepeatMasker .fa.out file. Could you please clarify? If this is an older output format from RepeatMasker, will Mobster accept the newer format, or how should this file be made?

Thank you, Nikki

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