[priyanka_15]

Tried to export PATH but still not worrking

Hi

I tried exporting the PATH But it is still not working ..PIctures attched

[GenoMax]

If trf is the file the program is trying to execute then $PATH directory declaration needs to end at the level of the directory which contains the trf file (e.g. /path_to/repeatscout/RepeatScout-1). Open a new terminal, re-export PATH and try again.

[priyanka_15]

ok , one more question should this be permanent ? because every time I close terminal it goes back to previous PATH..

I am new to this all ,perl,linux and repeatscout ; may be these are very easy questions

[priyanka_15]

Hello

I tried to do what you said ,is this the way ? It still is not reading the trf file

[GenoMax]

Two questions.

1. Have you compiled the software by doing "make" in this directory?
2. I see the following help when I try to run RepeatScout. Are you trying to follow directions given by someone/some website?

EDIT: I see that you are on step three of this process. You are trying to process the output of RepeatScount like this?

$ cat repeats.fa | filter-stage-1.prl > repeats-filtered.prl

[GenoMax]

Looking at the help further these are the steps involved. What steps have you completed?

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.

[priyanka_15]

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

[GenoMax]

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

[priyanka_15]

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 .

[priyanka_15]

Hi

I could run it this time but the fasta file is empty ..

[GenoMax]

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/

[priyanka_15]

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

[GenoMax]

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?

[priyanka_15]

yes ,no other error message and yes I did change the name to trf.

[priyanka_15]

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 ?