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How to split the Repetitive DNA file (rmsk) for human according to class and family using R

Hi,

I downloaded the Repetitive DNA file (rmsk) for human from UCSC website and I want to split this file according to class and family to get some basic statistics using R.

sequence genome next-gen
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updated by Ram Ram • written by M K M K

What have you tried and are you using the .out files or something from the table browser?

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written by Devon Ryan Devon Ryan

what kind of statistics, do you need the DNA sequences ?

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written by Pierre Lindenbaum Pierre Lindenbaum

I want to get some basic statistics like frequencies for each family to and class to compare this file with mouse to see if there is any relation between them according to families and classes.

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written by M K M K

2 answers

Using mysql ucsc (used mouse here, use hg19.simpleRepeat or hg19.nestedRepeat for human )

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D mm10 -e 'select repClass,repFamily,count(*) from rmsk group by 1,2'
+----------------+----------------+----------+
| repClass       | repFamily      | count(*) |
+----------------+----------------+----------+
| DNA            | DNA            |     1001 |
| DNA            | hAT            |     1949 |
| DNA            | hAT-Blackjack  |     4564 |
| DNA            | hAT-Charlie    |   105698 |
| DNA            | hAT-Tip100     |     9331 |
| DNA            | hAT-Tip100?    |      105 |
| DNA            | hAT?           |      585 |
| DNA            | MuDR           |      153 |
| DNA            | MULE-MuDR      |      583 |
| DNA            | PiggyBac       |      209 |
| DNA            | PiggyBac?      |      141 |
| DNA            | TcMar          |       52 |
| DNA            | TcMar-Mariner  |     1079 |
| DNA            | TcMar-Pogo     |       21 |
| DNA            | TcMar-Tc2      |     1786 |
| DNA            | TcMar-Tigger   |    35118 |
| DNA            | TcMar?         |      702 |
| DNA?           | DNA?           |     1027 |
| LINE           | CR1            |    14155 |
| LINE           | Dong-R4        |      138 |
| LINE           | L1             |   905176 |
| LINE           | L1?            |       52 |
| LINE           | L2             |    67909 |
| LINE           | RTE-BovB       |      260 |
| LINE           | RTE-X          |     1703 |
| LINE?          | Penelope?      |       42 |
| Low_complexity | Low_complexity |   386539 |
| LTR            | ERV1           |    71980 |
| LTR            | ERV1?          |      115 |
| LTR            | ERVK           |   319317 |
| LTR            | ERVK?          |     4185 |
| LTR            | ERVL           |   118061 |
| LTR            | ERVL-MaLR      |   454918 |
| LTR            | ERVL?          |      520 |
| LTR            | Gypsy          |     1859 |
| LTR            | Gypsy?         |      819 |
| LTR            | LTR            |      819 |
| LTR?           | LTR?           |      941 |
| Other          | Other          |    19450 |
| RC             | Helitron       |      345 |
| RC?            | Helitron?      |       74 |
| RNA            | RNA            |      691 |
| rRNA           | rRNA           |     1564 |
| Satellite      | centr          |        4 |
| Satellite      | Satellite      |    36865 |
| scRNA          | scRNA          |     8332 |
| Simple_repeat  | Simple_repeat  |  1015643 |
| SINE           | Alu            |   574557 |
| SINE           | B2             |   372923 |
| SINE           | B4             |   397726 |
| SINE           | Deu            |     1702 |
| SINE           | ID             |    64047 |
| SINE           | MIR            |   120436 |
| SINE           | tRNA           |     1618 |
| SINE?          | SINE?          |      274 |
| snRNA          | snRNA          |     3007 |
| srpRNA         | srpRNA         |      437 |
| tRNA           | tRNA           |     4769 |
| Unknown        | Unknown        |     6791 |
| Unknown        | Y-chromosome   |     2869 |
+----------------+----------------+----------+
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thank, Pierre. I did that, but how can I split the rmsk file in R I need the information for each class and each family separately.

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updated by Ram Ram • written by M K M K

If you really want to use R (using mysql is actually faster), then you just want the split() command.

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written by Devon Ryan Devon Ryan

I don't have experience for using mysql, also I want all information for each class and family like chr name, strand,...etc.

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updated by Ram Ram • written by M K M K

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