Re: [galaxy-user] Fastq to Bam conversion on paired end reads picard

[Kevin L]

Thanks! Got it to work
FYI
The data type was labelled as fastqcsanger although the extension
wasn't .fq (was
.fq_1) but it was listed in the first pull down menu

after I renamed it to .fq for both files, the second option didn't
automatically change to the first fastq file already.

Cheers
Kevin


On 22 October 2012 14:47, Jennifer Jackson  wrote:

> Hello,
>
> The tool will list all datasets of the appropriate input datatype in your
> history, including duplicates. The two must be the same and is set by the
> first dataset. For example, if the first is assigned as simply .fastq, the
> the second must be also be .fastq (and only .fastq datasets will be listed
> as potential inputs). If the first is .fastqsanger, the second must also be
> .fastqsanger.
>
> Modify datatypes as needed using the pencil icon -> Edit datasets ->
> Datatypes tab. Or, you may wish to use the "FASTQ Groomer" tool, if the
> data needs to be scaled to be Phred+33 (datatype .fastqsanger) - a format
> required by most of Galaxy's analysis tools. Please see the "FASTQ Groomer"
> tool form for the details. Data already scaled to Phred+33 can be safely
> set to .fastqsanger without running the groomer tool, although it can be
> helpful (option would be "Sanger") if you suspect a format issue, as it
> reports exactly where in the file the problem is located in the error
> message, but leaves the data unchanged (even when successful, e.g. no
> errors found).
>
> Hopefully this helps, but if your question has been misunderstood, please
> let us know, as we will probably need to examine your exact history/run
> conditions. I did quickly run a small test to check for a UI problem and
> didn't notice anything off with my samples.
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 10/21/12 7:38 PM, Kevin L wrote:
>
>> Hi
>> I was trying to enter the 2nd fq file into the second dialog box for
>> this tool but then the selection automatically changes to be the same as
>> the filename in the first dialog.
>>
>> is this a known issue?
>>
>> NGS: Picard (beta)
>> CONVERSION
>> FASTQ to BAM
>> >
>> creates
>> an unaligned BAM file
>>
>>
>> __**_
>> 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
>
___
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at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] Fastq to Bam conversion on paired end reads picard

[Jennifer Jackson]

Hello,

The tool will list all datasets of the appropriate input datatype in 
your history, including duplicates. The two must be the same and is set 
by the first dataset. For example, if the first is assigned as simply 
.fastq, the the second must be also be .fastq (and only .fastq datasets 
will be listed as potential inputs). If the first is .fastqsanger, the 
second must also be .fastqsanger.


Modify datatypes as needed using the pencil icon -> Edit datasets -> 
Datatypes tab. Or, you may wish to use the "FASTQ Groomer" tool, if the 
data needs to be scaled to be Phred+33 (datatype .fastqsanger) - a 
format required by most of Galaxy's analysis tools. Please see the 
"FASTQ Groomer" tool form for the details. Data already scaled to 
Phred+33 can be safely set to .fastqsanger without running the groomer 
tool, although it can be helpful (option would be "Sanger") if you 
suspect a format issue, as it reports exactly where in the file the 
problem is located in the error message, but leaves the data unchanged 
(even when successful, e.g. no errors found).


Hopefully this helps, but if your question has been misunderstood, 
please let us know, as we will probably need to examine your exact 
history/run conditions. I did quickly run a small test to check for a UI 
problem and didn't notice anything off with my samples.


Best,

Jen
Galaxy team

On 10/21/12 7:38 PM, Kevin L wrote:

Hi
I was trying to enter the 2nd fq file into the second dialog box for
this tool but then the selection automatically changes to be the same as
the filename in the first dialog.

is this a known issue?

NGS: Picard (beta)
CONVERSION
FASTQ to BAM
 creates
an unaligned BAM file


___
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
___
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/