Question: fastx_clipper problem in output
0
gravatar for mnmalash
2.5 years ago by
mnmalash0
mnmalash0 wrote:

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?

next-gen software error • 710 views
ADD COMMENTlink written 2.5 years ago by mnmalash0

show us the command line.

ADD REPLYlink written 2.5 years ago by Pierre Lindenbaum131k

fastx_clipper -k -n -v -i SRR123456.qualF.fastq -o SRR123456.qualF.clipped.fastq

ADD REPLYlink written 2.5 years ago by mnmalash0

It looks like you have not provided the adaptor string hence the program is looking for dummy default adaptor specified below.

[-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).
ADD REPLYlink written 2.5 years ago by Sej Modha4.7k

yes, I left it for default. is it required for functioning?

ADD REPLYlink written 2.5 years ago by mnmalash0

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).

ADD REPLYlink written 2.5 years ago by ATpoint42k

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?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by mnmalash0

Yes, skewer does all in one go. A typical command line for single-end data Illumina data could be:

./skewer -n -q 25 -Q 25 in.fastq.gz

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.

ADD REPLYlink written 2.5 years ago by ATpoint42k

this is awesome. Thank you dear

ADD REPLYlink written 2.5 years ago by mnmalash0
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