Results report: 002421_roreriPE_AGTCAA_L008_R1_all. fastq Results report: 002421_roreriPE_AGTCAA_L008_R1_all.fastq.gz FastQC Report AGRY 60000: Genomics

Warnig and failure in the last base of graphic. Problems: Warnig and failure in the last base of graphic. Clear with: TRAILING: Cut bases off the end of a read, if below a threshold quality. Warning A warning will be issued if the lower quartile for any base is less than 10, or if the median for any base is less than 25. Failure This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

The average quality above 27. No problems: The average quality above 27. Warning A warning is raised if the most frequently observed mean quality is below 27 - this equates to a 0.2% error rate. Failure An error is raised if the most frequently observed mean quality is below 20 - this equates to a 1% error rate. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems, the diference between A-T and C-G are less than 10% Warning This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position. Failure This module will fail if the difference between A and T, or G and C is greater than 20% in any position. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems with GC distribuition Warning A warning is raised if the sum of the deviations from the normal distribution represents more than 15% of the reads. Failure This module will indicate a failure if the sum of the deviations from the normal distribution represents more than 30% of the reads. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems with N content Warning This module raises a warning if any position shows an N content of >5%. Failure This module will raise an error if any position shows an N content of >20% . http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

warning – sequences of variable length Problems: warning – sequences of variable length And failure: no sequence with 0 lenght. Clear with MAXINFO: An adaptive quality trimmer which balances read length and error rate to maximise the value of each read . Warning This module will raise a warning if all sequences are not the same length. Failure This module will raise an error if any of the sequences have zero length. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems. Warning This module will issue a warning if non-unique sequences make up more than 20% of the total. Failure This module will issue a error if non-unique sequences make up more than 50% of the total. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Problems: sequence 1 overrepresented (0.37%). Clear with ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read. Warning This module will issue a warning if any sequence is found to represent more than 0.1% of the total. Failure This module will issue an error if any sequence is found to represent more than 1% of the total http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Problems: warning kmers overepresented in the sequence . Clear with:--Kmers Warning This module will issue a warning if any k-mer is enriched more than 3 fold overall, or more than 5 fold at any individual position. Failure This module will issue a error if any k-mer is enriched more than 10 fold at any individual base position. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Results report: 002421_roreriPE_AGTCAA_L008_R2_all. fastq Results report: 002421_roreriPE_AGTCAA_L008_R2_all.fastq.gz FastQC Report

Warnig and failure in bases 72-95. Problems: Warnig and failure in bases 72-95. Clear with: TRAILING: Cut bases off the end of a read, if below a threshold quality, or/ also CROP: Cut the read to a specified length by removing bases from the end. Warning A warning will be issued if the lower quartile for any base is less than 10, or if the median for any base is less than 25. Failure This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

The average quality are above than 27. No problems: The average quality are above than 27. Warning A warning is raised if the most frequently observed mean quality is below 27 - this equates to a 0.2% error rate. Failure An error is raised if the most frequently observed mean quality is below 20 - this equates to a 1% error rate. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Problems: diference between A-T greater then 10% in the position 1-2 . Clear with: LEADING: Cut bases off the start of a read, if below a threshold quality. Warning This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position. Failure This module will fail if the difference between A and T, or G and C is greater than 20% in any position. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems with GC distribuition. Warning A warning is raised if the sum of the deviations from the normal distribution represents more than 15% of the reads. Failure This module will indicate a failure if the sum of the deviations from the normal distribution represents more than 30% of the reads. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems with N content. Warning This module raises a warning if any position shows an N content of >5%. Failure This module will raise an error if any position shows an N content of >20%. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

warning – sequences of variable length Problems: warning – sequences of variable length And failure: no sequence with 0 lenght. Clear with MAXINFO: An adaptive quality trimmer which balances read length and error rate to maximise the value of each read. Warning This module will raise a warning if all sequences are not the same length. Failure This module will raise an error if any of the sequences have zero length . http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

No problems. Warning This module will issue a warning if non-unique sequences make up more than 20% of the total. Failure This module will issue a error if non-unique sequences make up more than 50% of the total. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Problems: sequence 1 overrepresented (0.41%) Clear with ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read. Warning This module will issue a warning if any sequence is found to represent more than 0.1% of the total. Failure This module will issue an error if any sequence is found to represent more than 1% of the total http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Problems: warning kmers overepresented in the sequence. Clear with:--Kimers. Warning This module will issue a warning if any k-mer is enriched more than 3 fold overall, or more than 5 fold at any individual position. Failure This module will issue a error if any k-mer is enriched more than 10 fold at any individual base position. http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf

Resources used: Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol Ecol. 2014 Apr;23(7):1679-700. doi:10.1111/mec.12680. http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf http://dnacore.missouri.edu/PDF/FastQC_Manual.pdf