Help with Summary Statistics
by D. A. Cowart
Hello,
I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 454 data. The
data has already been organized and sorted by species. The format of
the data is as follows:
>HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
tool/task available
via Galaxy?
Thank you,
Dominique Cowart
User name: dac330
8 years, 6 months
SNP finding
by Xiefan Fang
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences by
using Galaxy. In the next step, I want to find SNPs and calculate the SNP
percentage within the reads. There are 500,000 to 1,000,000 reads per
biological sample. Can I do it with galaxy? If not, is there other programs
available in windows? Considering that I am not very familiar with
programming.
Thanks,
Xiefan
University of Florida
9 years
queue rules for multi-step workflows
by zuzmus
Dear Galaxy managers,
I would like to ask about the queuing rules for the workflows before
processed on the server?
I use my customized Galaxy workflow which contains 22 following steps
(basically, filtering, trimming and format change of NGS data). I guess the
server is generally very busy during last weeks/months (?), so my job was
waiting about 24 hours in a queue (which would not be a problem), and then
the first step of the workflow was processed, but the following 21 is
again/still waiting (already for another couple of hours...). It makes me
wondering about the queuing rules because I expected that the whole
workflow is queued as one job.. Then my question is if the whole workflow,
once submitted, is listed in the queue, or does the following step queue
only after the previous step is finished (which would mean to wait the
whole queue for each step of the workflow...)?
I routinely used those wrokflows before (months ago) without any
problems...
I tried to search similar question in the archive before I posted this
one...
Thanks a lot for your answer,
My best
Zuzana Musilova
--
Zuzana Musilova, PhD.
(zuzmus(a)gmail.com)
Zoological Institute
University of Basel
Vesalgasse 1, CH-4051 Basel
Switzerland - Europe
9 years, 2 months
Connecting to new Galaxy Cloudman by FTP
by Mohammad Heydarian
Hi,
I am having trouble setting up a FTP connection with the recently released
version of Galaxy Cloudman (ami-118bfc78).
I have instantiated the new version of Galaxy Cloudman with
CloudLaunch<http://usegalaxy.org/cloudlaunch> and
also through the AWS EC2 wizard (using the same security group settings as
the previous versions) and neither instance will connect to my FTP
connection.
Has anyone else had this problem? Does anyone know what is preventing the
FTP connection?
Any help would be greatly appreciated.
Cheers,
Mo Heydarian
9 years, 3 months
FTP problem
by Karen Schwarzberg
Hello,
I am using the Galaxy server and I am trying to upload files. I do not see
the FTP option even when logged in. Please advise.
Best regards,
Karen
9 years, 3 months
rattus norvegicus reference genome
by Matthew Girgenti
Hi I'm currently using the Galaxy pipeline to analyze my illumina chip-seq data. When I try to use "NGA: Mapping>Map with Bowtie for Illumina" to map my reads there is no rat reference genome. I says I should contact galaxy. Should I simply upload the genome to proceed with analysis?
Thanks
Matt
9 years, 3 months
Problem with ftp connexion to Galaxy
by Fabrice BESNARD
Hello,
I registered some time ago to Galaxy.
>From the very beginning, my ftp connexion is not working.
I am using Filezilla, on a windows operating system. More precisely, the
connexion can be established, but the process fail when it is asking for
the password.
Statut : Résolution de l'adresse de main.g2.bx.psu.edu
Statut : Connexion à 128.118.250.4:21...
Statut : Connexion établie, attente du message d'accueil...
Réponse : 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP)
[::ffff:128.118.250.4]
Commande : USER fbesnard(a)biologie.ens.fr
Réponse : 331 Password required for fbesnard(a)biologie.ens.fr
Commande : PASS ***************
Réponse : 530 Login incorrect.
Erreur : Erreur critique
Erreur : Impossible d'établir une connexion au serveur
I sent an email two month ago to report this problem. I was answered that
this was an issue happening with the new accounts created.
Obviously, this issue has not been fixed yet, has it? If yes, could you
indicate me to make my ftp connexion works now ?
Thank you for your help !!
--
Fabrice Besnard
Institute of Biology of the Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75230 Paris cedex 05, France
8th floor. Office: Room 802. Lab: Room 817.
mail: fbesnard(a)biologie.ens.fr
Tel: +33-1-44-32-39-44
9 years, 3 months
Problem with downloading
by GANDRILLON OLIVIER
Hi
I am trying to download the results of my analysis (.sam files) from Galaxy main. The download gets interrupted about halfway, with no error message, as if the full file had been downloaded (but has not).
Thank's for your help
Best
Olivier Gandrillon
9 years, 3 months
SNPeff
by Andréanne Morin
Hello,
I would like to use SNPeff for annotation through GATK, However when I upload my file it seems like I cannot use it for this task. My file is .txt and is in this format :
Chr location ref allele alt allele
1 1234567 A T/C
What am I doing wrong?
Thanks,
Andréanne
9 years, 3 months
Filter fastq by percentage of ambiguous (N) bases
by Anto Praveen Rajkumar Rajamani
Hello,
I like to filter my fastq files (50 bp single end Illumina RNA seq reads) by a maximum threshold (10%) of ambiguous (N) bases.
I can see that the "CLIP" tool removes all reads with one or more N bases.
Is there a way to remove only the reads with five or more N bases using Galaxy?
Thank you.
Best wishes,
Anto
9 years, 3 months
