Peter and Guru;
[Computing GC]
I'll be working with simple sequence files (FASTA, or even FASTQ,
SFF, etc) rather than BED files, but I'll keep that in mind.
Emboss has some utilities that do this. infoseq and geecee, and
there are also programs for exploring CpG islands:
Yes it is - where you access the cloud console or Galaxy from has no affect
on running of the jobs.
Enis
On Thu, Apr 14, 2011 at 12:01 PM, Mike Dufault dufau...@yahoo.com wrote:
Hi,
I have an instance of Galaxy running on AWS. I would like to view it's
progress throughout the day, but I am
Hi Brad,
These tools are also in galaxy under the EMBOSS section. geecee
will tell you the percentage of GC in FASTA sequences. It basically
outputs the sequence name and then the GC content as below:
#Sequence GC content
Sequence1 0.44
Hope this helps!
Tychele
On Apr 14, 2011, at
Now why does a tool search on the public Galaxy instance for GC
not suggest this tool?
Name: geecee
Description: Calculates fractional GC content of nucleic acid sequences
Does this mean the description isn't searched? It would seem like
a sensible idea to me to include that...
The sys admin may need to bump up the digest size threshold for the
various lists. I only get galaxy-commits in digest form, but it's not
unusual for me to get three or four a day.
--
Olen
On Fri, Apr 8, 2011 at 11:09 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hi Yury,
You can manage your
Hi Olen, Yury, and all other digesters,
I've bounced the threshold for new digests up from 30KB to 300KB. Mailman
will still send out a digest at the end of the day, even if that threshold
is not hit.
Thanks for pointing this out.
Dave C.
On Thu, Apr 14, 2011 at 2:08 PM, Olen Vance Sluder Jr
Could someone take a look at this history in Galaxy?
http://main.g2.bx.psu.edu/u/kenaka/h/count-issue
collapser is not reporting the correct counts in the output for one of my
files. seqdata1 and seqdata2 should both have 50 reads. Yet it is reporting
more reads for seqdata1 in both the
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