Hi Veranja,
I am going to try to address all questions in one go since they are all
in the same thread. Next time though, it would be best send new
questions as a brand new question, not as a reply with just the subject
line changed. This helps us greatly with tracking and other users when
se
Hello Gema,
The tool group "GATK-Tools (beta)" is not indexed to function with the
hg19 genome.
As an alternative on the public Main Galaxy server, please see the tool
group " BEDTools". There are two tools here that calculate coverage
using BAM data as input.
Another alternative is to set
Hi Dipanjana,
I am not sure if you are still having trouble with upload or not, but if
your files are large, or even if you just want to track progress, using
FTP with a client is recommended.
http://wiki.galaxyproject.org/Support#Trouble_loading_data
My guess is that the upload jobs were wai
Hello Dipanjana,
I am not sure if you mean that the job is actually running (yellow) or
has been waiting in the queue (grey) during this time period (or some
combination), but I can let you know that both processes can vary in the
length of time they take to execute.
A job in the queue (grey
Hello Jianguang,
This setting is recommended to be used. It will merge all headers, but
if there are differences between the input files these will be combined
together in the final output. If you want to see what this content will
be, convert the BAM files before and after the merge to SAM f
> In addition to reducing the "the Minimum length of reas segments", do I also
> need to reduce "Anchor length" to get more mapping on splicing junctins?
Definitely worth a try.
> Looks like the setting for "Anchor length" only affects the number of mapped
> splicing junctions reported in the .
Hi Lizex,
It sounds like you are working on the command line and want to now
import data into Galaxy to work with it? If so, I'll add in an extra
comment to be careful about the reference genome when moving into Galaxy:
http://wiki.galaxyproject.org/Support#Rsync_data_and_moving_between_instan
Hi Jeremy,
Thank you for the information.
In addition to reducing the "the Minimum length of reas segments", do I also
need to reduce "Anchor length" to get more mapping on splicing junctins?
Looks like the setting for "Anchor length" only affects the number of mapped
splicing junctions report
Hi Andrew,
My first guess is that perhaps the region is not set correctly?
http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted
See "
Step 1: One Time Amazon Setup", subsection 2, where region is "
set your AWS Region to US East (Virginia)".
36bp reads will map across splice junctions but at a relatively low rate; you
can try changing segment length to get better mapping, but you'll want to
evaluate the results carefully to ensure that you're getting good results.
Good luck,
J.
On Apr 8, 2013, at 5:45 PM, Du, Jianguang wrote:
> Hi
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