Fastq to Bam conversion on paired end reads picard
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<https://main.g2.bx.psu.edu/tool_runner?tool_id=picard_FastqToSam> creates an unaligned BAM file
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 <https://main.g2.bx.psu.edu/tool_runner?tool_id=picard_FastqToSam> 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:
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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 <jen@bx.psu.edu> 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 <https://main.g2.bx.psu.edu/**tool_runner?tool_id=picard_**FastqToSam<https://main.g2.bx.psu.edu/tool_runner?tool_id=picard_FastqToSam>> 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<http://lists.bx.psu.edu/listinfo/galaxy-dev>
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://galaxyproject.org
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