Hi Larry,
If you are performing RNA-seq analysis, there is no need to filter the
data to ensure exact pairs before running Tophat. Later steps will deal
with any unpaired sequences.
If you are instead performing variant analysis, then in many cases you
will want matched pairs. Join the data first, perform any manipulations
that may remove reads entirely (filtering by quality), then split and
perform steps that may only trim off ends (if even needed). The FASTQ
splitter/joiner are at the top of the "NGS: QC and manipulation" tool
group, FASTQ Quality Trimmer is a bit lower down. Use FastQC to
understand what thresholds to use, per dataset.
Hopefully this helps,
Jen
Galaxy team
On 7/22/13 9:10 PM, Larry Simpson wrote:
Hi Users
How do I process paired reads from an Ilumina Miseq platform? If I
first use "Groomer" and then "Filter by quality", the paired reads get
out of sync. I read some responses to similar questions in this Forum
that the paired reads must first be "joined" before filtering and
then split for mapping. There is also a "Fastq interlacer" command to
join reads. However, I also read in the Forum that Galaxy requires the
filtered paired reads to be of equal length. But would not the
filtering process on the joined reads also modify the length of each
differently? Or can the NGS: Picard command "Paired Read Mate Fixer"
be used to re-synchronize the paired reads?
If there is no way around the requirement for equal lengths, then I
guess that it is really not possible to process paired reads in
Galaxy? But I am sure it is just my stupidity.
Full disclosure: Be kind, I am a novice in this field, just learning
Galaxy (which by the way is a fantastic resource!).
Larry Simpson
UCLA
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Jennifer Hillman-Jackson
Galaxy Support and Training
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
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please use the interface at:
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