User: muppetleague

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muppetleague10
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2 years, 5 months ago
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Posts by muppetleague

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Anyone with experience in the TE-annotation package REPET?
... Here is an install guide for the SGE queuing system, just remember to do a system reboot.  https://scidom.wordpress.com/2012/01/18/sge-on-single-pc/ In the MySQL setup, if you forget to set the database schema to MyISAM AFTER you try to run REPET, you must go back and delete the tables in MySQL an ...
written 2.8 years ago by muppetleague10
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Comment: C: Trying to modify new Repbase .embls to work as RepeatMasker .embl
... Oh yeah, it worked great! I had no reason to stay with the embl format, I just had a case of tunnel vision. ...
written 3.4 years ago by muppetleague10
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Comment: C: Trying to modify new Repbase .embls to work as RepeatMasker .embl
... Thanks for answering! Really appreciate your work on the Transposome program. I tried the -nois and -no_low (forget the exact characters of that flag) and then it stalled out on creating the SINE lib. I was unaware of the formatting script!  ...
written 3.4 years ago by muppetleague10
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Answer: A: permission denied error
... It looks like the file isn't set as an executable or you lack privileges for that directory. sudo chmod +x /media/C2F8EFBFF8EFAFB9/bedops-2.14.2/bin/gtf2bed If that doesn't work, try moving the executable off of the media device and into a new directory such as /usr/local/bin ...
written 3.4 years ago by muppetleague10
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Answer: A: how to identify same protien sequences in one fasta file
... Have you looked at UCLUST? http://www.drive5.com/usearch/manual/cmd_cluster_fast.html You can specify the identity threshold with -id and a decimal between 0 and 1 (such as -id 0.9) The filename specified in the -centroids option will contain the unique sequences.  ...
written 3.4 years ago by muppetleague10
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Trying to modify new Repbase .embls to work as RepeatMasker .embl
... Repbase has multiple releases a year, so I'm trying to build a script to reformat the concatenated .embls to a format similar to the last database released for RepeatMasker. Every line starts with a couplet that denotes the type of information contained. The nucleotide sequence lines are not shown b ...
transposable elements python repeatmasker repbase written 3.4 years ago by muppetleague10 • updated 3.4 years ago by SES8.1k
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Tophat/cuffdiff versus CLC for mapping RNA-seq reads
... I've noticed poor overlap between number of differentially expressed genes between CLC's 'Empirical Analysis of DGE' (edgeR test) versus Cuffdiff. CLC maps 20% more reads on average, and finds 200-400% more differentially expressed genes. It is to my understanding that CLC uses a proprietary read ma ...
tophat clc cuffdiff rna-seq edger written 4.2 years ago by muppetleague10 • updated 4.2 years ago by Dan D6.6k
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Answer: A: Programs to estimate divergence of RepeatMasker output
... I've gotten the RepeatMasker utility scripts to work nicely now, but I am unclear on the best way to infer a molecular clock from the Kimura 2-paramater divergence estimate. Any hint toward applying this to a more traditional phylogenetic approach (especially in light of the master gene copying hypo ...
written 4.5 years ago by muppetleague10
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Programs to estimate divergence of RepeatMasker output
... Hi all, I've been having trouble getting others' scripts to work with RepeatMasker output. The bundled RM script 'calcDivergenceFromAlign' gives an empty html file for RM's aln, and a garbled output for Censor's aln. REannotate looks very promising but hangs on my unmodified RM .out files for four s ...
reannotate repeatmasker written 4.6 years ago by muppetleague10

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