Entering edit mode
6.5 years ago
mnmalash
•
0
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?
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