Question: Data From History Now Showing Up In Fastq Drop Down
0
gravatar for Aarti Desai
6.0 years ago by
Aarti Desai90
Aarti Desai90 wrote:
Hi All, We have a galaxy local install. Thanks to Carlos's suggestion, I was able to get the reference genome index to show up in the interface. Now, I am trying to get the data into the galaxy system. I have followed the instructions in the link below to create data libraries. http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries I have modified the following sections in the universe_wsgi.ini file: # Add an option to the library upload form which allows administrators to # upload a directory of files. library_import_dir = /media/FreeAgent GoFlex Drive_/HDD1/Project # Add an option to the admin library upload tool allowing admins to paste # filesystem paths to files and directories in a box, and these paths will be # added to a library. Set to True to enable. Please note the security # implication that this will give Galaxy Admins access to anything your Galaxy # user has access to. allow_library_path_paste = True I created a data library and using the "Add dataset" function, I pasted the path of my data directory in the galaxy UI and selected the "link to files without copying into galaxy" option. This picked up all the files that were present in the directory and except for a couple of files, the job seems to have completed successfully. Now I am not sure how to actually analyze this data. I performed the "Import to current history" operation on two paired end fastq files I want to analyze. These show up in the history with the appropriate size. But when I choose the "Map with BWA for Illumina" option, the two fastq files do not show up in the FASTQ file drop down. These files do show up in the list of files for running fastqc I have also restarted the server after importing the data in the history, but the problem persists. Any input on how to go about analyzing the data in the local galaxy instance once it has been brought into the galaxy frame work is highly appreciated. Thanks for the help. Regards, Aarti Aarti Desai, Ph.D | Domain Specialist - Life Sciences aarti_desai@persistent.co.in<mailto:aarti_desai@persistent.co.in> | Cell: +91-9673009492 | Tel: + 91-20-67036348 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.com<http: www.persistentsys.com=""/> DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
bwa alignment • 1.3k views
ADD COMMENTlink modified 6.0 years ago by Luciano Cosme220 • written 6.0 years ago by Aarti Desai90
0
gravatar for Luciano Cosme
6.0 years ago by
Luciano Cosme220
Luciano Cosme220 wrote:
Hi, I believe you have to run Fastq Groomer first to convert it to sanger format. Then you will be able to see your dataset. https://main.g2.bx.psu.edu/u/dan/p/fastq Best, Luciano
ADD COMMENTlink written 6.0 years ago by Luciano Cosme220
Thanks. Sent from Samsung mobile Hi, I believe you have to run Fastq Groomer first to convert it to sanger format. Then you will be able to see your dataset. https://main.g2.bx.psu.edu/u/dan/p/fastq Best, Luciano DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
ADD REPLYlink written 6.0 years ago by Aarti Desai90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 95 users visited in the last hour