Question: Mapping a dataset of paired reads using BWA:MEM
gravatar for pegah.ghiabi
20 months ago by
pegah.ghiabi0 wrote:

I'm trying to run the BWA:MEM mapping tool on my paired data. My data has been already uploaded and saved in history. Once I open the dataset and try to run the tool, it does not add my FASTQ file to execute the job.

what would the problem be?


bwa mapping • 736 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by pegah.ghiabi0

An index need to be added to the 6 files saved under my history so I can proceed with further analysis.

Please help with this issue.


ADD REPLYlink written 20 months ago by pegah.ghiabi0
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Fastq data does not need to be indexed. Most tools only recognize fastq input that has the datatype "fastqsanger" assigned (leaving this as simply "fastq" will not work). Click on the pencil icon to assign this and see if that change brings up the fastq datasets in the tool form input list.

It was not exactly clear what is going on, so if you still need help, please explain a bit more about the problem. Where are you using Galaxy? At or elsewhere? What is the tool name and version (this is noted at the top of the tool form)? What is the datatype assigned to the input fastq datasets?

Thanks! Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson25k
gravatar for pegah.ghiabi
20 months ago by
pegah.ghiabi0 wrote:


Thanks for your email. I'll now give you some more info about the work I'm doing. I'm a new user with minimal experience working on and I'm trying to use BAM-MEM tool to align 3 paired sequence datasets to human genome.

I was able to upload and view my files in BWA tool after assigning them the "fastqsanger" datatype. Then, I carried on the analysis by aligning them to human genome with BWA-MEM tool. However, I cannot view the BAM results on my computer (Macbook) when I press the eye icon. Please note that I have already installed the BAM viewer on my computer.

My question is how can I visualize the alignment results and how I can interpret them. Thanks for your support.


ADD COMMENTlink written 20 months ago by pegah.ghiabi0
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