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Old 10-02-2015, 11:57 AM   #21
GenoMax
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Looking at the help further these are the steps involved. What steps have you completed?

Quote:
First, build_lmer_table
creates a file that tabulates the frequency of all l-mers in the
sequence to be analyzed. Second, RepeatScout takes this table and
the sequence and produces a fasta file that contains all the repetitive
elements that it could find. Third, the "filter-stage-1.prl" script
is run on the output of RepeatScout to remove low-complexity and
tandem elements; RepeatMasker is run on the sequence of interest using
this filtered RepeatScout library. The program "filter-stage-2.prl"
then filters out any repeat element that does not appear a certain number
of times (by default, 10). Finally, the locations of the repeats found
by RepeatMasker are used, in conjuction with GFF files that describe
segmental duplications or exons or other such "uninteresting" regions
to remove sequences from the library that are likely to not be mobile
elements; the program "compare-out-to-gff.prl" does exactly this.
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Old 10-02-2015, 11:58 AM   #22
priyanka_15
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Hi, yes I did compile it by make ..
I am trying to learn while doing this so I am using commands from the following link :
http://http://seqanswers.com/forums/showthread.php?t=5448
Yes, I am trying to fliter low complexity reads on stage 1.so this is my command:
cat kib_repeats.fa| ./filter-stage-1.prl >kib_repeats_filtered1.fasta
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Old 10-02-2015, 12:00 PM   #23
GenoMax
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Have you completed the first 2 steps? Did those run without errors? Can you post the commands you used for those steps? This post has a nice recap of the commands: http://seqanswers.com/forums/showpos...0&postcount=10
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Old 10-02-2015, 12:09 PM   #24
priyanka_15
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Hello

yes ,first two ran without error :
these are my commands for first two [./build_lmer_table -l 14 -sequence kib.fa -freq ~/Desktop/Kib15.freq
]
[/Storage_1/repeatscout/RepeatScout-1$ ./RepeatScout -sequence kib.fa -output kib_repeats.fa -freq Kib15.freq -l 14]
I did looked for the commands you have shown ,but I cannot solve this trf problem .
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Old 10-02-2015, 12:42 PM   #25
priyanka_15
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Hi

I could run it this time but the fasta file is empty ..
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Old 10-02-2015, 12:57 PM   #26
GenoMax
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You are going to have to install the TRF program from here: http://tandem.bu.edu/trf/trf.download.html Once that is done make sure the trf program is in your path or export TRF_COMMAND='/path_to/trf' is set.

You will need nseg as well. I think it is here: ftp://ftp.ncbi.nih.gov/pub/seg/

Last edited by GenoMax; 10-02-2015 at 01:05 PM.
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Old 10-02-2015, 01:22 PM   #27
priyanka_15
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I did downloaded the trf from here , and also have nseg there..

as i think trf is in path right now but empty file again and ahain
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Old 10-02-2015, 03:06 PM   #28
GenoMax
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No other error messages? I tried a small file and step 3 worked for me. Did you rename (or softlink) the executable from trf407b.linux64 to just trf?
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Old 10-02-2015, 05:48 PM   #29
priyanka_15
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yes ,no other error message and yes I did change the name to trf.
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Old 10-02-2015, 06:25 PM   #30
priyanka_15
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did u had nseg in your path too ? I just have it installed the same directory as trf , is that a difference ? should I try to export nseg path too ?
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Old 10-03-2015, 05:31 AM   #31
GenoMax
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If nseg is in your $PATH it should be ok. What happens if you just run

Code:
$ trf
Do you get the help for trf printed to screen?
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Old 10-06-2015, 10:03 AM   #32
priyanka_15
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Hello ,I was able to run this with all commands ,i did not compiled nseg properly...but I could run it then..

NOw, I have data from RepeatMAsker , the repeat library ,but it does not show any transpsosns in my genome...I ran it with RMBlast , do you think running with HMMER ,CROSS_MATCH would make a diff ?

also , any recommendations for transposon analysis ?
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Old 08-19-2016, 05:35 AM   #33
zhanghao
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Dear yzzhang

Have you resovled this problem? I came accross the same problem!

Quote:
Originally Posted by yzzhang View Post
Thank, suryasaha. I will try to use repeatscout directly for my assembly to see if the result is same as RepeatMoldeler log says. Many Thanks.
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Old 08-23-2016, 12:22 AM   #34
Macspider
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If you exported the RepeatScout-1 directory to your $PATH, you don't need to write ./filename.prl, you just need to write filename.prl. If you include "./", it will search it in the current directory and maybe that is the problem (just guessing, I'm not a RepeatScout user, this looks more like a shell problem!)
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