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Ben - I think I disagree.
I envision trimming 3' adaptor on an as needed basis - if the read aligns to the fasta database without trimming, then, then emit that alignment, otherwise trim as little as 3' adaptor as possible to make the alignment
such ability would be of benefit to how we're using bowtie
novoalign appears to have such a feature - however it is not "as needed"...
2009-11-10 21:18:21 UTC in Bowtie
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malcook committed revision 22193 to the Generic Model Organism System Database SVN repository, changing 1 files.
2009-10-26 16:19:47 UTC in Generic Model Organism System Database
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Annotation browser should support filtering
by selection (similar "sliced view"' > "slice by selection" feature)
by the value of any displayed column
For instance, I would like to only show annotations for a specific tier (i.e all my miRNA's only). Currently I do this by sorting on tier and then scrolling.
Great tool - Thanks - Malcolm.
2009-09-09 14:25:22 UTC in GenoViz
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ooops, I realize now I should have posted this under "Informatics Research k-mer Tools", which I have just done. Sorry!
2009-06-19 04:44:54 UTC in Whole-Genome Shotgun Assembler
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I am running the svn head on atac on the contig output of two assemblies --
they are the "LargeContigs.fna" from roche/newbler assemblies of 454
results.
The stderr output (attached) reports "finished" and provides path to .atac
and clumps.atac files. completion.
Examination of these files however shows they only contain the header.
There is no tabular data.
Any suggestions for how to...
2009-06-19 04:43:57 UTC in Informatics Research k-mer Tools
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I am running the svn head on atac on the contig output of two assemblies -- they are the "LargeContigs.fna" from roche/newbler assemblies of 454 results.
The stderr output (attached) reports "finished" and provides path to .atac and clumps.atac files. completion.
Examination of these files however shows they only contain the header. There is no tabular data.
Any suggestions for how to...
2009-06-19 04:31:30 UTC in Whole-Genome Shotgun Assembler
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Here is a patch
Index: makeplot.pl
===================================================================
--- makeplot.pl (revision 1802)
+++ makeplot.pl (working copy)
@@ -51,7 +51,7 @@
print GP "set grid\n";
print GP "unset key\n";
print GP "set border 10\n";
-print GP "set tics scale 0\n";
+print GP "set ticscale 0\n";
print GP "set xlabel \"REF\"\n";
print GP "set ylabel \"AS.
2009-06-19 03:40:12 UTC in Informatics Research k-mer Tools
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running atac.pl is giving me an error with gnuplot integration
I am running the latest gnuplot - gnuplot.x86_64 4.0.0-12
here is the error I get:
gnuplot> set tics scale 0
^
"/mec/atac/10v200/stats/woContaminant10KvswoContaminant200K.matches.gp", line 5: ';' expected
any suggestions?
Thanks!
2009-06-17 23:12:21 UTC in Informatics Research k-mer Tools
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it would be great to have support for -d and -u as implemented for blastcl3
-d Database [String] default = nr
-u Restrict search of database to results of Entrez2 lookup [String] Optional
with -d you you can choose databases besides nt - like EST databases - who could live without?
with -u you can limit search by organism which is nice (you could provide list of organisms...
2009-03-03 17:07:17 UTC in Generic Model Organism System Database
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Coming across this late in the game but thought to chime in anyway....
it might help to have in your toolkit the perl module Bio-Trace-ABIF which provides for read and writeback to ab1 files editted and uneditted sequence and quality scores. (PBAS1 PBAS2 PCON1 PCON2)
-Malcolm Cook.
2009-02-28 07:54:54 UTC in AMOS
