trouble Clipping barcodes on data
by KAKOLIE GOSWAMI
Dear Galaxy Users,I have a data set, for which I'm trying to "Clip" adapter
sequences. After splitting the generated data based on different Barcode
sequences, I clip the adapter sequences off. This method worked for all the
other data sets that I worked with, but seems to act up with one particular
data set. I rechecked the sequence and did everything that I could think of to
remove this problem, but the error message remains the same as following. Can
anyone please help me on this.
<http://main.g2.bx.psu.edu/history>##An error occurred running this job:
gzip: Segmentation fault
stdout: Broken pipe
Thanks,Regards
Kakolie Goswami
Graduate Student
9 years, 1 month
Re: [galaxy-user] Need help with local install of Galaxy
by Jennifer Jackson
Hello Aarti,
On 9/12/11 1:26 AM, Aarti Desai wrote:
> Hi Jennifer,
> I have previously used the web version of Galaxy for doing some RNASeq analysis and I loved it!
>
> I now have some more RNASeq and ChIPSeq data I want to analyze using Galaxy, but the file sizes are more than 2GB and hence am unable to use the web version.
Larger data can be loaded onto the public Galaxy main instance at
http:/usegalaxy.org using FTP as described:
1 - on the "Get Data -> Upload" tool form, lower section
2 - in this wiki example document
http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP
3 - in the screencast example "Tool tutorials -> Using FTP"
http://galaxyproject.org/wiki/Screencasts
More help can be obtained starting from:
http://galaxyproject.org/wiki/Learn
> I have got Galaxy installed on a server a couple of weeks back, but have not been able to use it at all. I get stuck at the stage of trying to upload the files. After some time I get an internet connection timeout error. My files are between 3 - 6 Gb in size. Will anybody from your team be able to help with this issue?
>
> I am sending this directly to you but if you feel this is more appropriate for the mailing list, I will be happy to send it out there, but am getting a little bit desperate trying to get Galaxy to work.
You are correct, the mailing list is the best place to ask questions. I
will forward this question & reply to the galaxy-user mailing list, as
others may encounter similar issues and will benefit from the reply. In
the future, using a mailing list to asks questions would be appreciated.
http://galaxyproject.org/wiki/Support
> Would greatly appreciate your help.
> Regards,
> Aarti
Take care,
Jen
Galaxy team
>
>
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
9 years, 1 month
Installing Galaxy on my computer
by Lilach F
Hi,
I am a new user of Galaxy.
I want to analyze whole human exome data with Galaxy and cannot upload the
files (10 Gb each) to the server.
Should I install Galaxy on a PC, and work in Unix environment, or there is a
more comfortable way?
If I should install it - what should be the computer properties, and where
can I find the instructions for using it? I found the instructions for
installing in Wiki, but didn't find the what computer is should be (RAM, HD,
etc).
Thanks,
Lilach
9 years, 1 month
Trimming small RNA
by Thiago Mafra
Hello everybody,
I have sequences of small RNA's from 18 to 35nt and accurate trim the
sequences of the adapters before aligning the reads with the reference
genome. Are there any tools available to it in the Galaxy?
Thanks.
--
Thiago Mafra Batista
Biólogo Molecular
Doutorando em Bioinformática - UFMG
LGB - ICB/Bloco K4 sala 245
Tel Lab: (31) 3409-2628
CV: http://lattes.cnpq.br/9414909432933240
9 years, 1 month
Chip-Seq, Encode Peaks and Galaxy
by Radhouane Aniba
Hi everyone,
I have a list of genomic regions with some variants and would like to study
the correlation between theses variants and epigenomics marks such as
histone modifications.
>From Encode download page, i got some files corresponding to peaks of these
hsitone modifications and would like to know if there is a way to create a
pipeline using galaxy to map my variants, depending on genomic regions to
the information I have from the histone modification peaks.
Is there someone who can point me to a step by step to do things to start
using Galaxy ?
Thank you
Rad
9 years, 1 month
running cufflinks
by Jennifer Jackson
===> Please use "Reply All" when responding to this email<===
Hello,
File type can be set by using a dataset's pencil icon to reach the "Edit
Attributes" form. GTF and GFF are both very similar. It is possible that
the 9th field ("group" for GFF, "attributes" for GTF) was not detected
automatically upon upload or that there is some problem with format to
double check (extra tabs or whitespace).
Hopefully this helps,
Best,
Jen
Galaxy team
On 9/6/11 1:29 PM, Peng, Tao wrote:
> Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY
> ensemble were recognized by GALAXY cufflinks as a GTF file although they
> all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as
> GFF files?
>
> Thx,
>
> tao
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
9 years, 1 month
Extracting reads mapped from bwa mapping
by Austin Paul
Hello,
I recently figured out how to filter the output bwa SAM file for flag type
in order to determine the number of reads that were successfully mapped. My
question is, I previously thought I could generate a pileup, then sum the
number of counts for each base of the reference, and divide this number by
the length of the reads (not exact if some reads are hanging over the edge
of the reference sequence, but should be close?). But when I compare these
methods, I get drastically different results. What am I missing?
Thanks,
Austin
9 years, 1 month
Gene Track
by Neal DeLuca
After using Mac, and clicking on view in Gen Track an error pops up saying:
You're seeing this error because you have DEBUG = True in your Django settings file. Change that to False, and Django will display a standard 500 page.
How are these setting changed?
Neal
9 years, 1 month
