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Question: Fastq To Bam Conversion On Paired End Reads Picard
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gravatar for Kevin Lam
6.1 years ago by
Kevin Lam • 70
Kevin Lam • 70 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
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modified 6.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.1 years ago by Kevin Lam • 70
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gravatar for Jennifer Hillman Jackson
6.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k
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
ADD REPLY • link written 6.1 years ago by Kevin Lam • 70
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