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

2. 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.

3. 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.

4. 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.

5. 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.

6. 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% .

7. 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.

8. 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.

9. 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

10. 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.

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

12. Warnig and failure in bases 72-95.
Problems:
Warnig and failure in bases
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.

13. 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.

14. 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.

15. 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.

16. 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%.

17. 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 .

18. 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.

19. 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

20. 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.

21. Resources used:
Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol Ecol Apr;23(7): doi: /mec