Question: Re: Getting Reference Index Files In Local Galaxy Install
0
Aarti Desai • 90 wrote:
Hi,
We have a local install of galaxy and I'm trying to add the reference
index files for bwa using the information provided in the following
link
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
I have modified the bwa_index.loc file present in the ../tool-data
directory by adding the path to where the index is on our server (Also
attached). However, even after restarting the server, the reference
genome does not show when choosing the "use a built-in index option".
I'm not sure whether the loc file is correctly created and whether any
other configuration file needs to be changed/updated. Help in the
matter greatly appreciated.
Thanks,
Aarti
To: Lindsey Kelly
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Initial QC and grooming for Illumina
HiSeq2000 paired end RNAseq data
Hello Lindsey,
Yes, you have this correct. The general path would be to:
- join forward and reverse data per run
- run FASTQ Groomer & FastQC
(note: if your data is already in Sanger FASTQ format with Phred+33
quality scaled
values, the datatype '.fastqsanger' can be directly assigned and
the FASTQ Groomer
step skipped. This is likely true if your data is a from the latest
CASAVA pipeline, but
please double check.)
- discard data as needed based on quality
- split forward and reverse data that passes QC
- concatenate all forward reads from a sample into one FASTQ file
- concatenate all reverse reads from a sample into one FASTQ file.
- for each sample, run TopHat using the two concatenated FASTQ files
To manipulate paired end data, please see the tools -> NGS: QC and
manipulation: FASTQ splitter & FASTQ joiner.
To combined data files head-to-tail from multiple runs into a single
FASTQ file please see the tool -> Text Manipulation: Concatenate
datasets.
I am not sure of the actual volume of data, but if these start to get
large or TopHat errors with a memory problem, a local or cluster
instance would be the recommendation: http://getgalaxy.org
For reference:
http://tophat.cbcb.umd.edu/manual.html
http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
Hopefully this helps. Others are welcome to post comments/suggestions.
Jen
Galaxy team
I am trying to do RNAseq analysis on Paired end data from the
Hiseq2000. I have about 50 files for each sample (25 forward and 25
reverse - although each sample has a different number of files).
I think that I need to:
-convert them into FASTQ sanger format using the FASTSQ groomer tool
-check the quality using the FASTQqc tool
I don't know how to handle this many files. Do I have to groom and
run the QC for each file? Should I join the paired files and run both
tools on each pair, or should I combine all of the data for each
sample (which I don't know how to do) and then groom and run the QC
for all of the reads for the sample.
Thanks in advance for advice
Lindsey
___________________________________________________________
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
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 COMMENT
• link
•
modified 6.4 years ago
by
Avik Datta • 20
•
written
6.4 years ago by
Aarti Desai • 90
