Hi, what I want to get is if I give rna long read fastq file as input, I would like to get all the read length of its file. Most files just give mean or median read length of the file (e.g. 880 bp ONT, 2200 bp PacBio) It would be nice to get read length distribution of the fastq file.
Tools for read length distribution
Is there a tool to check the read length distribution (not just the mean or median) in the long reads fasta file? I would like to plot the distribution and see enrichments for very specific length. Or can this be done by command tool easily?
1 answer
check the read length distribution (not just the mean or median) in the long reads fasta file?
If you have the sequencing summary file available from the Nanopore run you can use pycoQC (LINK).
I would like to plot the distribution and see enrichments for very specific length.
You can only estimate enrichment after aligning the data but what does specific length have to do with that? Are you looking for a specific product (amplicon?) of a certain length?
You get an overview of the distribution in pycoQC but if you need a full list of lengths then you can use the solutions in this thread: Sequence Length Distribution From A Fastq File
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