Thanks for this nice tool!
I have a question about FastQC output. I would like to see the base quality statistics for each base position over my read length, but the output I'm getting is in bins. Are there any options to control this output?
The bins from the run on my data are individual bases from 1-9, then a bin for 10-14, 15-19, etc. The text output is below... where the column shows "#Base", but clearly this corresponds to the bin number (the bins are shown in the image produced) and not the base number.
>>Per base sequence quality pass
#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
1 37.91416393670764 39.0 38.0 39.0 36.0 39.0
2 37.7802692498972 39.0 38.0 39.0 36.0 39.0
3 37.75980052781196 39.0 38.0 39.0 36.0 39.0
4 37.72458631487738 39.0 38.0 39.0 36.0 39.0
5 37.64205081404644 39.0 37.0 39.0 35.0 39.0
6 37.70586245218606 39.0 38.0 39.0 36.0 39.0
7 37.66601699162634 39.0 37.0 39.0 35.0 39.0
8 37.64294997657492 39.0 37.0 39.0 35.0 39.0
9 37.62989555748825 39.0 37.0 39.0 35.0 39.0
10 35.65410371880296 37.4 34.6 39.0 29.2 39.0
11 27.368080692355903 27.8 22.6 33.0 17.2 36.6
12 32.93512849552606 35.6 29.8 38.2 23.0 38.6
13 36.13160789430458 38.0 35.4 39.0 31.2 39.0
14 36.36371473707043 38.0 36.0 39.0 32.4 39.0
15 36.05634409485578 38.0 36.0 39.0 31.2 39.0
16 35.925524253742545 37.8 36.0 39.0 31.2 39.0
17 35.6997651658535 37.2 35.4 39.0 30.6 39.0
18 35.28466949479758 37.0 35.0 39.0 29.8 39.0
19 34.77657154343021 37.0 34.4 39.0 28.6 39.0
20 34.148071746563744 36.8 33.8 39.0 27.0 39.0
21 33.42794421987793 36.0 33.0 38.8 24.8 39.0
22 32.38145771412453 35.6 31.8 37.2 21.6 39.0
23 32.798688106416485 36.6 32.6 38.4 21.8 39.0
24 32.71342747797581 36.8 32.6 38.8 20.0 39.0
25 31.64278511180337 36.0 31.2 38.4 7.8 39.0
26 30.307687847194188 35.6 29.4 37.8 2.0 39.0
27 28.901251293483632 35.0 27.4 37.0 2.0 39.0
28 27.45705418439078 34.0 24.0 37.0 2.0 39.0
Because I only have data for bins, it makes it hard to decide what base to trim my data to when there is a problem.
What do you think?
I have a question about FastQC output. I would like to see the base quality statistics for each base position over my read length, but the output I'm getting is in bins. Are there any options to control this output?
The bins from the run on my data are individual bases from 1-9, then a bin for 10-14, 15-19, etc. The text output is below... where the column shows "#Base", but clearly this corresponds to the bin number (the bins are shown in the image produced) and not the base number.
>>Per base sequence quality pass
#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile
1 37.91416393670764 39.0 38.0 39.0 36.0 39.0
2 37.7802692498972 39.0 38.0 39.0 36.0 39.0
3 37.75980052781196 39.0 38.0 39.0 36.0 39.0
4 37.72458631487738 39.0 38.0 39.0 36.0 39.0
5 37.64205081404644 39.0 37.0 39.0 35.0 39.0
6 37.70586245218606 39.0 38.0 39.0 36.0 39.0
7 37.66601699162634 39.0 37.0 39.0 35.0 39.0
8 37.64294997657492 39.0 37.0 39.0 35.0 39.0
9 37.62989555748825 39.0 37.0 39.0 35.0 39.0
10 35.65410371880296 37.4 34.6 39.0 29.2 39.0
11 27.368080692355903 27.8 22.6 33.0 17.2 36.6
12 32.93512849552606 35.6 29.8 38.2 23.0 38.6
13 36.13160789430458 38.0 35.4 39.0 31.2 39.0
14 36.36371473707043 38.0 36.0 39.0 32.4 39.0
15 36.05634409485578 38.0 36.0 39.0 31.2 39.0
16 35.925524253742545 37.8 36.0 39.0 31.2 39.0
17 35.6997651658535 37.2 35.4 39.0 30.6 39.0
18 35.28466949479758 37.0 35.0 39.0 29.8 39.0
19 34.77657154343021 37.0 34.4 39.0 28.6 39.0
20 34.148071746563744 36.8 33.8 39.0 27.0 39.0
21 33.42794421987793 36.0 33.0 38.8 24.8 39.0
22 32.38145771412453 35.6 31.8 37.2 21.6 39.0
23 32.798688106416485 36.6 32.6 38.4 21.8 39.0
24 32.71342747797581 36.8 32.6 38.8 20.0 39.0
25 31.64278511180337 36.0 31.2 38.4 7.8 39.0
26 30.307687847194188 35.6 29.4 37.8 2.0 39.0
27 28.901251293483632 35.0 27.4 37.0 2.0 39.0
28 27.45705418439078 34.0 24.0 37.0 2.0 39.0
Because I only have data for bins, it makes it hard to decide what base to trim my data to when there is a problem.
What do you think?
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