User: hlyates

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hlyates0
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Posts by hlyates

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Comment: C: How to filter FASTQ by QS & length using galaxy tools in the command line?
... My supervisor asked me to do it. I was able to groom and trim already. I have the source files of galaxy downloaded and I reference galaxy in an PYTHONPATH in the scripts I wrote. What makes fastq_filter not easy to use from the commandline is how it takes another script for an argument, but doesn't ...
written 3.3 years ago by hlyates0
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Comment: C: How to filter FASTQ by QS & length using galaxy tools in the command line?
... Thank you for your reply.The xml confirms what I read in the source code. Namely, that we have to use a line like this: fastq_filter.py $input_file $fastq_filter_file $output_file $output_file.files_path '${input_file.extension[len( 'fastq' ):]}' I am still stuck, I don't know how to make $fastq_f ...
written 3.3 years ago by hlyates0
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How to filter FASTQ by QS & length using galaxy tools in the command line?
... Problem I am stuck on how to implement filtering on the command line using the galaxy tools. Specifically, I want to do this for the command line. I want to use the following filtering parameters: Input parameter: value Minimum size: 40 Maximum size: 0 Minimum Quality: 30 Maximum Quality: 0 ...
filtering galaxy fastq qs commandline written 3.3 years ago by hlyates0 • updated 3.3 years ago by Bjoern Gruening5.1k

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