I want to know the standard value of quality score or sequence length in trimming by fastx_toolkit.
In my RNA-Seq textbook, author trim fastq sequences whose base quality scores are under 20 and lengths become under 30bp (original length is 100 bp). Is that the standard value or changes case by case ?
If there is standard value of quality score or sequence length that many biologist adopt, please tell me that value. Also, if it changes case by case, please tell me how biologist judge and decide its value.
1 answer
Bases affiliated with a phred score less than 20 have more than 1% chance of being incorrectly sequenced.
This score is oftenly used because below this threshold, the bases are judged as "bad" by fastqc.
But firstly you can run a fastqc to see the quality of the raw fastq files. If the data are bad, you can decrease this score to not delete too many reads
Log in to answer this question.
-
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
written by Κοσμάς •
-
NGS Sequence quality
written by samrendra.thakur01 •
-
BLAST e-value between two sequences vs BLAST e-value between sequence and data base
written by nyanovsky •
-
cannot understand coverage function in Granges package
written by alexmondaini •
-
WGCNA
written by artepapa •
-
Cufflinks takes too long time on my PC
written by takoyaki
-
Please advise me on PE sequencing reads prepared by NEBNex kit and Hiseq2000
written by seta
-
NGS Fastqc explanation
written by GHanumanth404 •
-
How to tune blast parameters when looking for miRNAs?
written by seta
-
Fastq Quality Check
written by toshnam
There is no standard for these things since every dataset is different. You will need to experiment and find out what your dataset looks like on QC. If you have a good reference to align to, you may be able to use data down to Q15.
If possible omit using
fastx_toolkitwhich, is old by NGS standards.bbduk.shfrom BBMap suite,trimmomaticorcutadaptare all great alternatives.