[galaxy-user] tophat deletions output
dear all, how can we use the tophat deletions output? e.g. if I want to see and conpare between two samples if a specific gene or transcript had been deleted, how can I use this output? is visualisation enough? thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Files uploaded via FTP - 530 Sorry, the maximum number of clients (3) for this user are already connected.
Hi, I am trying to upload new files to galaxy via FTP using Filezilla. I have this error message: 530 Sorry, the maximum number of clients (3) for this user are already connected. What can I do? Julie -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] cuffdiff sample values assigned
On 8/21/12 4:33 AM, i b wrote: Thanks Jen, useful link. But I did not understand one thing. I have the following FPKM in cufflinks for two samples: s1 (untreated): 1234106 s2 (treated): 159713 cuffdiff of the two samples gives me the following values: value_1:5.4 value_2:20.9 and it is not significant (!). My two question: 1. how is this not significant? 2. what is the realtion between the high fpkm in cufflinks and the low values in cuffdiff?I read the manual: is this part of the statistical method adopted?e.g are these numbers (cuffdiff values) derived from the formula adopted? thanks a lot, ib On Thu, Aug 16, 2012 at 11:26 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello, A very similar question came up a few days ago and Jeremy had some good advice for how to approach learning to interpret this data: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-August/004985.html Best, Jen Galaxy team On 8/15/12 8:49 AM, i b wrote: Dear all, in cuffdiff outputs e.g. transcript differential expression, I find for example: value_1 value_2 log2(fold_change) 7.77183 0 -1.79769e+308 or value_1 value_2 log2(fold_change) 0 14.5972 1.79769e+308 for many many rows. if I sort in excel my data by fold change column (big to small ), all the rows with -1.79769e+308 or +1.79769e+308 are on the top. How can be sure that these on the top are really the most up-regulated or down regulated transcripts if I don't know the real value of one of the two samples (is 0 really zero?)? I was told that the zero in one if the two samples is very small number and Cuffdiff simply writes 0, but it is not absolutely zero, otherwise it would not be possible ot have -1.79769e+308 or 1.79769e+308 Could you please tell me then how can I extrapolate the highest fold change? (up and down regualted)?or of what is done by sorting by log fold chnage is correct? Thanks, ib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] run Bowtie to estimate Mean Inner Distance between Mate Pairs
Howdy Jianguang,
There's a more complete description of the SAM format in The Sequence
Alignment/Map format and SAMtools, Li et al, Bioinformatics (2009). And
you can find the latest specification for the format at
samtools.sourceforge.net .
In the spec, the terminology for the ISIZE field has been changed to TLEN,
template length, to allow for sequencing technologies that produce more
than two sequenced segments. The description there is the number of
bases from the leftmost mapped base to the rightmost mapped base.
So I think to convert to inner distance between mate pairs you would
typically take ISIZE and subtract the lengths of the mates. Note that for
some technologies that value could be negative (which just means the mates
overlap). You might need to take into account whether the mates have been
mapped with proper orientation-- for example, if an inversion has flipped
one mate it has also carried that mate closer to or farther from the
other.
Bob H
Hello Jianguang,
On the Bowtie tool form itself, please find this text:
Outputs
The output is in SAM format, and has the following columns:
Column Description
1 QNAME Query (pair) NAME
2 FLAG bitwise FLAG
3 RNAME Reference sequence NAME
4 POS1-based leftmost POSition/coordinate of clipped sequence
5 MAPQ MAPping Quality (Phred-scaled)
6 CIGAR extended CIGAR string
7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
8 MPOS 1-based Mate POSition
9 ISIZE Inferred insert SIZE
10 SEQquery SEQuence on the same strand as the reference
11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
12 OPTvariable OPTional fields in the format TAG:VTYPE:VALUE
The value of ISIZE is the total insert size for this read pair.
Hopefully this helps!
Jen
Galaxy team
On 8/16/12 2:34 PM, Du, Jianguang wrote:
Dear All,
In order to figure out the Mean Inner Distance between Mate Pairs of my
paired-end RNA-seq datasets, I ran Bowtie (Map with Bowtie for Illumina)
with both forward and reverse datasets and mouse mm9 as reference
genome. Below I list the Bowtie output for only one pair of reads (I put
the fields on the left side):
For the forward read
...snip...
Is the ISIZE the insert size? The difference between POS and MPOS is
145bp, which is 36bp shorter than ISIZE (181). My question is: if
ISIZE does mean insert size, how should I convert INSIZE into Mean Inner
Distance between Mate Pairs?
Thanks,
Jianguang Du
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[galaxy-user] Aggregate collections of files (example: Heatmaps)
I am developing several tools that will need to read and write multiple data files at once. For example, Eisen Cluster produces a heatmap which consists of three files: a .cdt file, .atr file and a gtr file which are the underlying heatmap and the array tree and the gene tree. All three files need to be kept together. I guess I could wrap them in a zip file and pack and unpack them. The heatmap is not just a view only object. Some tools, such as cuttree, would extract one tree and then aggregate genes (or arrays) below a certain depth and create a new trio of files. Is there support for (or plans for creating) any aggregate data types? Thanks Ted CBSE, UCSC ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Files uploaded via FTP - 530 Sorry, the maximum number of clients (3) for this user are already connected.
Hi Julie, This was mostly likely an issue on our side. Please try to FTP again and let us know if you continue to have problems. Our apologies for the inconvenience, Jen Galaxy team On 8/21/12 3:23 AM, Julie Rodor wrote: Hi, I am trying to upload new files to galaxy via FTP using Filezilla. I have this error message: 530 Sorry, the maximum number of clients (3) for this user are already connected. What can I do? Julie -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] FTP upload problem
Hi, I am trying to upload 12 fastq files to Galaxy via FTP. The FTP is randomly loosing connection, caussing interruption of the upload. Can you let me know what is wrong? Thanks, fatih ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] How to find the alternatively spliced segment of genes in Cuffdiff output
Dear All, I have run programs from Tophat to Cuffdiff of Galaxy to look for the difference in alternative splicing events between cell types. However I do not know how to find the detail information (such as the sequence and the genomic coordinates) of the alternatively spliced part of a given gene. I looked at the data of Cuffdiff ouput splicing differential expression testing, there is no column showing the position of alternatively spliced region. Please help to solve this problem. Thanks in advance. Jianguang Du ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Aggregate collections of files (example: Heatmaps)
On Tue, Aug 21, 2012 at 4:46 PM, Ted Goldstein t...@soe.ucsc.edu wrote: I am developing several tools that will need to read and write multiple data files at once. For example, Eisen Cluster produces a heatmap which consists of three files: a .cdt file, .atr file and a gtr file which are the underlying heatmap and the array tree and the gene tree. All three files need to be kept together. I guess I could wrap them in a zip file and pack and unpack them.The heatmap is not just a view only object. Some tools, such as cuttree, would extract one tree and then aggregate genes (or arrays) below a certain depth and create a new trio of files. Is there support for (or plans for creating) any aggregate data types? Hi Ted, There is support for composite datatypes, so this should be possible. http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes This kind of discussion is normally directed to the galaxy-dev list (CC'd) Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] New reference genome in Bowtie
Dear All, I was wondering if it would be possible to add Mycobacterium tuberculosis H37Rv as a reference genome to the list of built-in indexes in the Map with Bowtie for Illumina (version 1.1.2) tool. Thank you, Sarah ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] How to upload multiple files......
Hi, I've recently installed galaxy. I was trying to find how to upload multiple files without the need to compress them into a zip/gz file first. Is this possible? As the Get Data option allows only one file at a time. I searched the galaxy archive mailing list but didn't find anything conclusive. I am unable to use ftp client tools due to IT restrictions. Thanks Neil ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] FTP upload problem
Hi, I have been having FTP issues for the past several days. I am using Filezilla. The upload starts, then stops after about 32MB and the connection closes and tries to reopen, then closes again. I also tried the command line ftp client in win7 with same results. rich From: Jennifer Jackson j...@bx.psu.edu To: Fatih Ozsolak fatihozso...@gmail.com Cc: galaxy-user@lists.bx.psu.edu Sent: Tuesday, August 21, 2012 12:51 PM Subject: Re: [galaxy-user] FTP upload problem Hi Faith, There was an FTP issue on our side earlier today, but your processing does not quite fit the usual symptoms. Please try to FTP again using a client that will allow interrupted transfers to be resumed (FileZilla, CyverDuck) see if that helps. You might also want to check your general internet connection - there are several speedtest type tools that can detect problems. Use google to locate one or if you have a system administrator they should be able to help. Very sorry to hear that you are having problems but hopefully one of these options will help, Jen Galaxy team On 8/21/12 9:34 AM, Fatih Ozsolak wrote: Hi, I am trying to upload 12 fastq files to Galaxy via FTP. The FTP is randomly loosing connection, caussing interruption of the upload. Can you let me know what is wrong? Thanks, fatih ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] LimitInternalRecursion
Hi, There's this error message in my apache log: [error] Request exceeded the limit of 10 subrequest nesting levels due to probable confguration error. Use 'LimitInternalRecursion' to increase the limit if necessary. Use 'LogLevel debug' to get a backtrace., referer: ... When I turn the apache debug log on it also shows: [debug] core.c(3072): r-uri = /galaxy/proxy: http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/root/history_item_updates, referer: ... It seems like mod_rewrite is somehow misconfigured, but I couldb't figure out what it is. Here is my httpd.con mod_rewrite conf: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /opt/bioinformatics/share/galaxy-central/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /opt/bioinformatics/share/galaxy-central/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /opt/bioinformatics/share/galaxy-central/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] Could you please help me to debug this? Thank you, Adhemar ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] file upload renamed
When uploading a file using “Get Data” it seems the file is renamed to
dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to keep
its name rather than being renamed?
It seems this is being done because of the line
${output.dataset.dataset.id}:${output.files_path}:${file_name}
in the upload.xml file. But I don't know where in the code it gets ${file_name}
from. Any ideas how i change this to get the correct name of the file being
uploaded?
Neil
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