fastx_clipper problem in output
I use fastx_clipper to clip adapters from FASTQ files after quality filtering using Fastq_quality_filter, but the output file is empty while after execution it says how much the input and output were and how much too short reads it discarded. what could be wrong?
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mnmalash •
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show us the command line.
fastx_clipper -k -n -v -i SRR123456.qualF.fastq -o SRR123456.qualF.clipped.fastq
It looks like you have not provided the adaptor string hence the program is looking for dummy default adaptor specified below.
yes, I left it for default. is it required for functioning?
Do not use fastx-toolkit in 2018. It is not actively being maintained and does not support paired-end data (as far as I know). Currently accepted options are bbdup.sh from BBMap, trimmomatic, cutadapt or skewer (the latter is my go-to choice).
Thanks for the nice recommendations. I have read about skewer as you recommended and I see it makes quality filtering. Does this mean I don't need quality filtering by other methods such as pearf or even fastq_quality_filter of fastx-toolkit and it will do both functions at once?
Yes, skewer does all in one go. A typical command line for single-end data Illumina data could be:
It removes reads with excessive Ns (-n), removes bases at the 3' end until it hits a base with quality > 25 (-q 25) and discards reads with an average base quality below 25 (-Q 25). Supports multithreading (-t numberCores) and offers compression (-z) of the trimmed reads.
this is awesome. Thank you dear