flaking regions across TSS
by shamsher jagat
I am interested in getting regions flanking TSS, I am using Glaxaxy and
have downloaded TSS sites using
this post steps
https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html
Now what I would like to do is to get 5000 bp upstream an
downstream using flank tool in galaxy, but i realize it only gave me option
for gene start or whole gene.
Is it possible to extract 5000 bp upstream and downstream regions across
tss start site . Once I have that then I want to find non overlaping genes
in my regions from chipseq data.
Thanks
Kanwar
8 years, 2 months
cuffdiff biological replicates
by i b
Hi guys,
a bit of confusion about how to give cuffdiff certain outputs:
having 1 control and 8 tumour samples which I consider biological
replicates (not technical replicates), how shall give the input to
cuffdiff?
If I want to use cuffcompare as gtf: shall I cuffcompare all 8samples
plus the control and then run cuffdiff using this gtf?
When adding the bam files, shall I have to make 8 groups plus control groups?
or one groups with 8 bams and second group with the control bam?
Much appreciated an answer!!
Thanks
ib
8 years, 2 months
cuffdiff: same gene listed with different FPKM values
by i b
Dear all,
has anything like this happened to you?
I compared two samples with cuffdiff and when I look at the
differentially expressed genes values I have the same gene listed for
5 times with different values.
E.g.
sample1 sample2 gene
71.6837 9.76435 NM_005514
87.6456 27.3965 NM_005514
115.333 4.81687 NM_005514
38.1879 5.2753 NM_005514
69.4197 5.84387 NM_005514
112.964 3.89226 NM_005514
What does this mean? And how do I know which one represents the real
expression level for that gene for the two samples?
Thanks,
ib
8 years, 2 months
gene or transcript differential expression testing
by i b
Hi,
I am a bit confused about two outputs of cuffdiff:
If I want to see if two samples, e.g. treated and un-treated express
similar protein levels, what would be best to look at gene
differential expression or transcript diff. expression?
Thanks,
ib
8 years, 2 months
metagenomic workflow
by Asuncion Lago
Hi,
I am trying to analyse my eukaryotic metagenome data using yours workflow
for windshield splatter analysis. But I find several problems:
1- it is related to "draw phylogeny", this tool fails always for most of my
samples, reporting the error: incorrect tree structure. Tree string position
341
2- It is related with the "summarize taxonomy" step. I this case I obtain
results but the number of counts are too high compared with the original
reads. My samples are small, around 8000 reads and the counts obtained are
more that 200000 for some phyla. I guess this is not ok, as far as I
understand from your paper than counts are equivalent to reads, am I right?
3- another strange thing is the fact that the number of sequences increase
after run the step for select the high quality segments. Any reason for
this???
I will really appreciate you help. Thanks in advance
Asun
8 years, 2 months
SAM Tools Pileup
by So, Kathy GZ/US
Hi,
I'm having trouble with the Generate Pileup tool and hope that you could
help me troubleshoot this. I ran the tool successfully with the
following options:
* Use built-in index
* Print the mapping quality as the last column
* Print all lines
* Cap mapping quality = 60
* Call consensus = yes, then default parameters
The reference bases of the entire pileup file, however, are all "N." I
double checked and the all the files have the same reference genome
(mm9). Do you have any ideas on what went wrong?
Thanks very much for your help,
Kathy
Kathy So
Genzyme Corp.
Functional Genomics
49 New York Ave.
Framingham, MA 01701
508-271-4717
8 years, 2 months
The GATK has a new website and forum
by Geraldine Van der Auwera
Hi everyone,
Just a quick email to let you know that the GATK has a new website and
forum.
The new website, released in parallel with GATK version 2.0 (beta) features
a much improved documentation system and user-friendly introductory
materials for new users. Also, the forum is now integrated into the website
and linked to the documentation, making it much easier to refer to the docs
in forum discussions and find relevant information.
If you hated the old Wiki, you're going to love this.
http://www.broadinstitute.org/gatk/
8 years, 2 months
All I want is a question answered please!
by Jennifer Jackson
Hi Crystal,
The galaxy-user(a)galaxy.bx.psu.edu mailing list would be the best for
this question. All lists are described here:
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
http://wiki.g2.bx.psu.edu/Mailing%20Lists
Grey jobs are scheduled to run the and aere in the queue. While they are
waiting to run, it is important to not start and restart, as this
effectively movest them to the end of the line@
Hopefully this helps,
Jen
Galaxy team
On 7/26/12 8:57 AM, Crystal Marconett wrote:
> Hello,
>
> I am trying desperately to get an answer to a question. I've been over the help area for an hour trying to find an email address to ask questions to, and the only one is the tophat people's email... which is not helpful, because the problem is starting the tool in Galaxy, not getting TopHat errors yet because the job is simply stuck on grey (waiting......)
>
> The question:
> I am trying to start running tophat on my history in the Galaxy main wed interface. I started the job last night at 10pm. It's now 9am. The job is still "waiting to run", ie. grey. How long does it take the Tophat web interface to start? is there a data limit that above which Tophat can no longer run? I don't think this is right, I've run TopHat before on Galaxy with the Illumina whole body tissue data and it took a while, but not this long....
>
> My username is: cmarcone(a)usc.edu
> the History's name is: Per-RNAseq
> The job is : #32, 33, 34, 35 (all grey Tophat for Illumina).
> The history has 65.7GB in it, and says it is using 21% (I assume the amount of allocated space left on the server).
>
> Please help! And if this is not the right e-mail address can you forward this along to the correct one, please!!! or at least let me know the correct email to mail this too.
> Thanks!
> C
--
Jennifer Jackson
http://galaxyproject.org
8 years, 2 months
CloudMan - Can't start nodes
by mailing list
Hi guys,
I created a new Galaxy instance (probably around early July) with the
web launcher (https://biocloudcentral.herokuapp.com/launch).
I've been coming back and re-using it since then. However for the
past week at least I haven't been able to launch new nodes. They show
up as red on the indicators, and below I've pasted the error messages.
(Could this be related to a new version of cloudman being released?)
Thanks,
Greg
This is the cluster status log from my last attempt:
15:55:02 - Retrieved file 'persistent_data.yaml' from bucket
'cm-[redacted]' to 'pd.yaml'.
15:55:02 - Master starting
15:55:05 - Completed initial cluster configuration.
15:55:25 - Prerequisites OK; starting service 'SGE'
15:55:37 - Configuring SGE...
15:55:37 - Setting up SGE did not go smoothly, running command 'cd
/opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned
code '1' and following stderr: ''
15:55:57 - Saved file 'persistent_data.yaml' to bucket 'cm-[redacted]'
15:55:57 - Trouble comparing local (/mnt/cm/post_start_script) and
remote (post_start_script) file modified times: [Errno 2] No such file
or directory: '/mnt/cm/post_start_script'
15:55:58 - Adding 2 instance(s)...
15:57:32 - Instance 'i-56ba942e' reported alive
15:57:33 - Successfully generated root user's public key.
15:57:33 - Sent master public key to worker instance 'i-56ba942e'.
15:57:47 - Adding instance 'i-56ba942e' as SGE administrative host.
15:57:47 - Process encountered problems adding instance
'i-56ba942e' as administrative host. Process returned code 2
15:57:47 - Adding instance 'i-56ba942e' to SGE execution host list.
15:57:47 - Process encountered problems adding instance
'i-56ba942e' as execution host. Process returned code 2
15:57:47 - Problems updating @allhosts aimed at adding
'i-56ba942e', running command 'export SGE_ROOT=/opt/sge;.
$SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf
-Mhgrp /tmp/ah_add_15_57_47' returned code '2' and following stderr:
'/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh '
15:57:47 - Waiting on worker instance 'i-56ba942e' to configure itself...
15:57:47 - Instance 'i-54ba942c' reported alive
15:57:47 - Sent master public key to worker instance 'i-54ba942c'.
15:58:01 - Adding instance 'i-54ba942c' as SGE administrative host.
15:58:01 - Process encountered problems adding instance
'i-54ba942c' as administrative host. Process returned code 2
15:58:01 - Adding instance 'i-54ba942c' to SGE execution host list.
15:58:01 - Process encountered problems adding instance
'i-54ba942c' as execution host. Process returned code 2
15:58:01 - Problems updating @allhosts aimed at adding
'i-54ba942c', running command 'export SGE_ROOT=/opt/sge;.
$SGE_ROOT/default/common/settings.sh; /opt/sge/bin/lx24-amd64/qconf
-Mhgrp /tmp/ah_add_15_58_01' returned code '2' and following stderr:
'/bin/sh: 1: .: Can't open /opt/sge/default/common/settings.sh '
15:58:01 - Waiting on worker instance 'i-54ba942c' to configure itself...
8 years, 2 months
Re: [galaxy-user] "Jobs is waiting to run" all day on Main
by Lu, Mengmeng
Same problem here.
I want to add a custom build, but it has been processing for more than 5 hours. Is it normal?
PS: my reference genome which I used to add the custom build is about 42Mb.
Thank you.
Mengmeng
----- Original Message -----
From: "Mengmeng Lu" <mira0501(a)neo.tamu.edu>
To: "Lee Silver" <lsilver(a)genepeeks.com>
Sent: Sunday, July 22, 2012 2:45:52 PM
Subject: Re: [galaxy-user] "Jobs is waiting to run" all day on Main
Same problem here.
I want to add a custom build, but it has been processing for more than 5 hours. Is it normal?
PS: my reference genome which I used to add the custom build is about 42Mb.
Thank you.
Mengmeng
----- Original Message -----
From: "Lee Silver" <lsilver(a)genepeeks.com>
To: galaxy-user(a)bx.psu.edu
Cc: "Lee Silver" <lsilver(a)genepeeks.com>
Sent: Saturday, July 21, 2012 5:20:19 PM
Subject: [galaxy-user] "Jobs is waiting to run" all day on Main
Since earlier today (at least 6 hours), all of my jobs have been stuck in the "waiting to run" state on the Main Galaxy server.
Lee Silver
(leemsilver(a)genepeeks.com)
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8 years, 2 months
