Question

why all the reads in fastq files have the same quality value?

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6.8 years ago

bright602 ▴ 50

Hi there, could any one tell me why all the reads in my fastq file have the same or very similar quality value as showing below? Thanks a lot.

@NB502075:3:H2FM3BGX3:1:11101:9808:6370 2:N:0:TAGAACAC TTCGCCTAGTGGGAGCTTATCTTCTCGCCACCCTCGGTGGAAATGCCTCCCCATCTGCACAAGATGTCTTTAAGG + AAAAAEEE/EEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE @NB502075:3:H2FM3BGX3:1:11101:7933:6371 2:N:0:TAGAACAC TCAGGATTCTTTGAGTCTTGGATAATGGCTCCCGCTCGTAAGGGAAAGGCTAAGGAGGAACAGGCTGTCGTGTCC + AAAAAEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE @NB502075:3:H2FM3BGX3:1:11101:19490:6372 2:N:0:TAGAACAC TCGTAGGTGACGGGTTTTTCCTATGCCGAAAGGTATCGGTAAACCGTTGAAATTCTTCCATGTCCGGGATAGGGT + AAAAAEEE/EEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE @NB502075:3:H2FM3BGX3:1:11101:3601:6372 2:N:0:TAGAACAC ACGTCAACTCTACGCTGGCGTAAATCAATGTTGGAAACACTCGAAGAACAACGAAAAGCCGTCGAAGGTGAAGCA + AAAAAEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE @NB502075:3:H2FM3BGX3:1:11101:16612:6373 2:N:0:TAGAACAC AGTGCTGTTACCATTAGGACTGACAGATTGAAAGCTCTTTCTCGATTTGGTGGTTGGTGGTGCATGGCCGTTCTT + AAAAAEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

RNA-Seq sequence sequencing • 2.8k views

ADD COMMENT • link updated 6.8 years ago by Devon Ryan 104k • written 6.8 years ago by bright602 ▴ 50

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Where did they come from? Straight off the machine?

ADD REPLY • link 6.8 years ago by Joe 21k

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Follow up the original question, when I ran through fastqc, there is no error bar in the per base sequence quality. So the graph looks not usual.

ADD REPLY • link 6.8 years ago by bright602 ▴ 50

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Plase use ADD COMMENT instead of answer unless you are actually answering your own post.

ADD REPLY • link 6.8 years ago by Joe 21k

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Indeed. I have now moved his answer to a comment.

ADD REPLY • link 6.8 years ago by WouterDeCoster 47k

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Can you provide a bit more information about the sequences? What sort of machine? What library size/type of sequencing is it? Does all of your data look like this?

ADD REPLY • link 6.8 years ago by Joe 21k

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The machine ID is for a NextSeq ("NBXXXXXX").

ADD REPLY • link 6.8 years ago by Devon Ryan 104k

score 1 · Answer 1 · 2017-07-03

Since this is a NextSeq machine, please note that base qualities are binned into a few discrete values in that machine. For that reason, as long as the library is reasonably good quality, you'll relatively rarely see the error bars in FastQC reach much past 1 bin (a change of 5 on the Phred scale). For comparison, I just pulled a random sample from a recent NextSeq run and see 0 variance for the first ~30 or 75 bases in FastQC. I only see a yellow box in the last base. If you have a really messy library then you'll get more variance in that plot.