Repeatmasker output match input

Question

[Kian]

Hi my input file to UCSC for repeat elements is like:

chrom  txStart  txEnd
chr1    15079913    35209257

output:

genoName    genoStart    genoEnd    strand    repName    repClass    repFamily**
chr1    16777160    16777470    +    AluSp    SINE    Alu
chr1    25165800    25166089    -    AluY    SINE    Alu
chr1    33553606    33554646    +    L2b    LINE    L2

the raw of input file and output file is not the same. output have more raw in not the same the distance in input file!! how i can match two file?

How I have repeats elements for the default distance in input file and not more? Thanks

Answer 1

[Devon Ryan]

Why would you believe that a ~20 megabase region would all be exactly one type of repeat? That wouldn't be biologically plausible. The output from UCSC is correct, your assumption and goal is what's wrong.

[Kian]

Thanks for your response, i know in this distance there are not one type repeat, Actually, i want to know in the distance how many and what repeat exist. but i think UCSC divide my distance and tell me in the per section what repeat exist. its good but not my goal! in have a distance and want to know in this distance there are how many LINE, how many SINE, how many....,

[Devon Ryan]

It's giving you the individual entries, so count them. Alternatively, download the repeatmasker file, convert it to BED, use bedtools intersect and use whatever method you prefer to finish summarizing things.

[Kian]

Thanks, i will try it!