4:02 p.m.
Edward,
If you just want to conacatenate the fastq files (I assume that is what you mean) you can
do that using the text manipulation tools: concatenate datasets tail-to-head.
Good luck.
Alex
________________________________________
Van: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] namens
Edward Turk [edwardturk(a)mac.com]
Verzonden: zaterdag 24 december 2011 3:30
Aan: galaxy-user(a)lists.bx.psu.edu
Onderwerp: [galaxy-user] Merge FASTQ Databases
Hi Galaxy Users,
Can FASTQ Databases be merged using Galaxy?
Thanks,
Edward
___________________________________________________________
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/
10:47 p.m.
Alex,
Thanks that worked. I was thrown off by the word concatenate, which I mistakenly thought
would join reads together (reads remain separate), and by the absence of the word merge,
which is used when referring to combining two BAM datasets together in Galaxy. It seems to
me that the tool to combine BAM datasets, "Merge Bam Files", and the tool to
combine FASTQ datasets, "Concatenate datasets" work the same but
"Concatenate datasets" works on any type of dataset.
Edward
On Dec 27, 2011, at 11:02 AM, Bossers, Alex wrote:
Edward,
If you just want to conacatenate the fastq files (I assume that is what you mean) you can
do that using the text manipulation tools: concatenate datasets tail-to-head.
Good luck.
Alex
________________________________________
Van: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] namens
Edward Turk [edwardturk(a)mac.com]
Verzonden: zaterdag 24 december 2011 3:30
Aan: galaxy-user(a)lists.bx.psu.edu
Onderwerp: [galaxy-user] Merge FASTQ Databases
Hi Galaxy Users,
Can FASTQ Databases be merged using Galaxy?
Thanks,
Edward
___________________________________________________________
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/
3:30 p.m.
New subject: Data upload
Dear galaxy Users
I am very very new to galaxy, will be highly obliged if some one could help me to find the
way to analyse bacterial tramnscriptome. in the first step itself , i am having trouble to
upload files...
Does any one knows how to generate URL to upload data, my fastq files are about 3 gb each,
Is there any specific pipeline to analyse bacterial transcriptome
Thanking all of you
Ateeq
1:38 p.m.
New subject: Data upload
Ateeq,
The preferred method for uploading large files (that aren't already hosted somewhere)
is FTP. See the instructions here: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP
We don't generally provide specific analysis pipelines, rather the tools for composing
them, though you're welcome to look through the shared workflows, histories, and pages
(See "Shared Data" in Galaxy) for examples and perhaps someone else will chime
in with their experiences analyzing bacterial transcriptomes.
Lastly, try not to piggyback on unrelated threads (as in your other email). It makes
tracking email replies more difficult.
-Dannon
On Jan 9, 2012, at 10:30 AM, Ateequr Rehman wrote:
Dear galaxy Users
I am very very new to galaxy, will be highly obliged if some one could help me to find
the way to analyse bacterial tramnscriptome. in the first step itself , i am having
trouble to upload files...
Does any one knows how to generate URL to upload data, my fastq files are about 3 gb
each,
Is there any specific pipeline to analyse bacterial transcriptome
Thanking all of you
Ateeq
___________________________________________________________
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/
3827
days inactive
3845
days old
galaxy-user@lists.galaxyproject.org
4 comments
4 participants
participants (4)
-
Ateequr Rehman -
Bossers, Alex -
Dannon Baker -
Edward Turk