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Old 10-06-2015, 06:16 PM   #1
priyanka_15
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Location: new mexico

Join Date: May 2015
Posts: 17
Default output is 0 for most .tbl file in repeatmasker output

Hello

I ran repeatmasker for my 12MB bacterial genome with rmblast and I got this result :
ile name: kib.fa
sequences: 1
total length: 12113479 bp (12113479 bp excl N/X-runs)
GC level: 67.83 %
bases masked: 458056 bp ( 3.78 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 0 0 bp 0.00 %
ALUs 0 0 bp 0.00 %
MIRs 0 0 bp 0.00 %

LINEs: 0 0 bp 0.00 %
LINE1 0 0 bp 0.00 %
LINE2 0 0 bp 0.00 %
L3/CR1 0 0 bp 0.00 %

LTR elements: 0 0 bp 0.00 %
ERVL 0 0 bp 0.00 %
ERVL-MaLRs 0 0 bp 0.00 %
ERV_classI 0 0 bp 0.00 %
ERV_classII 0 0 bp 0.00 %

DNA elements: 0 0 bp 0.00 %
hAT-Charlie 0 0 bp 0.00 %
TcMar-Tigger 0 0 bp 0.00 %

Unclassified: 1973 385656 bp 3.18 %

Total interspersed repeats: 385656 bp 3.18 %


Small RNA: 0 0 bp 0.00 %

Satellites: 0 0 bp 0.00 %
Simple repeats: 1693 79440 bp 0.66 %
Low complexity: 0 0 bp 0.00 %
==================================================

* most repeats fragmented by insertions or deletions
have been counted as one element


The query species was assumed to be homo
RepeatMasker version open-4.0.5 , sensitive mode

run with rmblastn version 2.2.23+
The query was compared to unclassified sequences in "kib_repeats_filtered1.fasta"
RepBase Update 20150807, RM database version 20150

Can anyone help me why I am getting this reulst ?
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Old 10-07-2015, 03:39 AM   #2
GenoMax
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Moving this post to a new thread since it was not related to the original thread it was in.

@Prianka: Keep in mind that just because a command ran (and produced output) does not mean that the output is correct/right. Based on your last posts it appeared to me that even though you had managed to run RepeatScout/Repeatmasker the analysis may not have worked right.
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Old 10-07-2015, 05:14 PM   #3
priyanka_15
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Ok... then what would you suggest doing next ?
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