Question: FASTAQ not able to be selected in BWA, though FastaQC passed
1
gravatar for bon1068
16 months ago by
bon106830
bon106830 wrote:

I need some help. I am trying to map two fastq datasets with Bwa-mem. If I design a workflow by: Input dataset > FastQC > BWA-Mem, then just selecting the two raw fastq data and I am able to run and get the FastQC data and BWA results successful, with the default. However, If I run step-by-step to (1)FastQC, (2) BWA, I cannot select input dataset in BWA since it said there is no fastqsanger file available from the pull-down thus unable to run the BWA. Furthermore, If I manually change the datatype of FastQC's output's rawdata from txt to fastsanger (since the webpage of FastQC result shows good score and Pass QC), the BWA-MEM page shows the list of selection of input dataset is "Fastqc on data ..." (fastsanger)" but not my raw data Fastq file, but running the BWA will be unsuccessful with fatal code and exit.

Can anyone help to explain this and guide me to go through ? Thanks.

fastq workflow bwa fastqc • 456 views
ADD COMMENTlink modified 16 months ago by chen.randy110 • written 16 months ago by bon106830

Both answers below are correct. Here is how to determine which to use is appropriate for your data (includes video): https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

ADD REPLYlink written 16 months ago by Jennifer Hillman Jackson24k
3
gravatar for chen.randy
16 months ago by
chen.randy110
chen.randy110 wrote:

Change the datatype of the uploaded FastQ sequence from "fastq" to "fastqsanger" directly.

ADD COMMENTlink written 16 months ago by chen.randy110
1
gravatar for jm.keith
16 months ago by
jm.keith60
jm.keith60 wrote:

You may need to run your files through the FastQGroomer tool to put them into the correct format

ADD COMMENTlink written 16 months ago by jm.keith60
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