Options for verifying phred+33 format: https://www.biostars.org/p/63225/
If your dataset is already sanger format then in galaxy it is possible to assign ".fastqsanger" type to this data avoiding the grooming step.
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Originally posted by GenoMax View PostAs long as you know the reads are in sanger format (phred+33) you can go on to trimming/filtering.
- It seems the data is 100 cycle SE from high output: 1 lane (Illumina HiSeq 2500)
- They did trimming from sanger to sanger data?
- How can I verify myself that this is phred+33 format?
Did they make a mistake in grooming? It seems to me that Illumina HiSeq fastq data is not sanger? Or am I totally n00b?
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Originally posted by GenoMax View PostYou can get the code galaxy uses here (individual tools likely have other dependencies and it may not be simple to run them on the command line): https://toolshed.g2.bx.psu.edu/repos/devteam
As long as you know the reads are in sanger format (phred+33) you can go on to trimming/filtering.
That being said, thank you so much Geno. You've been a lot of help and I want you to know this. Have a great day.
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You can get the code galaxy uses here (individual tools likely have other dependencies and it may not be simple to run them on the command line): https://toolshed.g2.bx.psu.edu/repos/devteam
As long as you know the reads are in sanger format (phred+33) you can go on to trimming/filtering.
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Originally posted by GenoMax View PostThere is no need to "groom" if your reads are already in sanger format.Groomed 28403332 sanger reads into sanger reads
If so, my question is how can I obtain the tools galaxy uses for trim and filter for local commandline processing? Thank you for your patience and prompt answer.
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There is no need to "groom" if your reads are already in sanger format.
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How to perform grooming that galaxy does but on the commandline?
How do I groom sanger reads into sanger reads on my local commandline using the same tool that galaxy has found here?
In other words, I would like to do the following:- Obtain the same tool galaxy uses for grooming locally
- Invoke this tool on my local commandline
- Figure out how to use this tool on an entire directory of fastq files
I of course went to galaxy and I only saw a reference to a paper, but I don't know where to obtain the tool?
Thank you very much for reading this post.
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