Fastq to BAM file

1

Hi, I have been trying to follow the galaxyproject tutorial about sambam-datasets, however, when I try to map bwa-mem my fastq file, it does never run. It return with the error message that it could not align. What step shall I take? What would I be doing wrong?

Here the exactly message: file does not contain alignment data

By the way, here it is the tutorial that I have been following exactly. Manipulating NGS data with Galaxy - Galaxy Community Hub.

2

Dear pauloalabarse,
Please make sure you selected the correct reference (either from Galaxy or from your local history) and also check if you fastq files are correctly formatted.

Here is another tutorial that might help you: Mapping

Cheers,
Florian

1 Like
3

Dear Florian,

Thank you for your response. I tried to use FastQ Groomer before starting the Map step, and it worked. Thank you again.

Paulo.