fq.gz file use
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4.3 years ago

I am novice so maybe my questions looks stupid.

I want use fq,gz file in R. So I decompress it by gunzip() then it became .fq format file. How can I use .fq.gz file?

And I wonder can I open .fq.gz file in BioEdit? Please answer. Thank you

BioEdit R • 6.2k views
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I want use fq,gz file in R.

What do you want to do with it?

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I receive assembly result so I want check it.

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An assembly is not in an fq.gz file. What you are looking at are most probably just individual reads.

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If you have the *.fq, why do you still want to use the *.gz specifically?

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nope, just I don't know how can treat those files.

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Maybe try bioconductor ShortRead. It can read .fq.gz.

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ok, thank you for your answer.

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And I wonder can I open .fq.gz file in BioEdit.?

No you probably can't do that.

If you are thinking of doing a multiple sequence alignment from your fastq file then you will at a minimum need to convert your fastq format reads to fasta format. Does wanting to use BioEdit make a specific sense? Are you sequencing amplicons where your fastq reads could potentially be used for a MSA?

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I want to make assembly pipeline with Illumina template. Is it possible?

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I would advise you to spend some time reading up on sequence assembly. Go and read the manual for a tool like Spades, or if you already have a reference, MIRA.

If you just want to use your reads to check the accuracy of an existing assembly (since you’ve told us several different things so far) then you need to read up on remapping (e.g. via BWA or Bowtie).

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