diff --git a/Help/3 Analysis Modules/1 Basic Statistics.html b/Help/3 Analysis Modules/1 Basic Statistics.html index 76766aa..33623cc 100644 --- a/Help/3 Analysis Modules/1 Basic Statistics.html +++ b/Help/3 Analysis Modules/1 Basic Statistics.html @@ -21,8 +21,8 @@

Summary

  • File type: Says whether the file appeared to contain actual base calls or colorspace data which had to be converted to base calls
  • Encoding: Says which ASCII encoding of quality values was found in this -file. -
  • Total Sequences: A count of the total number of sequences processed. +file.
  • +
  • Total Sequences: A count of the total number of sequences processed. There are two values reported, actual and estimated. At the moment these will always be the same. In the future it may be possible to analyse just a subset of sequences and estimate the total number, to speed up the analysis, diff --git a/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html b/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html index 7597d58..08a07ea 100644 --- a/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html +++ b/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html @@ -28,7 +28,7 @@

    Summary

    can see that certain tiles show consistently poor quality. A good plot should be blue all over.

    -

    Kmer profiles

    +

    Per tile quality

    Reasons for seeing warnings or errors on this plot could be transient problems such as bubbles going through the flowcell, or they could diff --git a/Help/3 Analysis Modules/4 Per Base Sequence Content.html b/Help/3 Analysis Modules/4 Per Base Sequence Content.html index bae1142..b4dd69b 100644 --- a/Help/3 Analysis Modules/4 Per Base Sequence Content.html +++ b/Help/3 Analysis Modules/4 Per Base Sequence Content.html @@ -59,7 +59,7 @@

    Common reasons for warnings

    1. Overrepresented sequences: If there is any evidence of overrepresented sequences such as adapter dimers or rRNA in a sample then these sequences -may bias the overall composition and their sequence will emerge from this plot. +may bias the overall composition and their sequence will emerge from this plot.
    2. Biased fragmentation: Any library which is generated based on the ligation of random hexamers or through tagmentation should theoretically have good diversity through the sequence, but experience has shown that these libraries @@ -67,7 +67,7 @@

      Common reasons for warnings

      due to a biased selection of random primers, but doesn't represent any individually biased sequences. Nearly all RNA-Seq libraries will fail this module because of this bias, but this is not a problem which can be fixed by processing, and it -doesn't seem to adversely affect the ablity to measure expression. +doesn't seem to adversely affect the ablity to measure expression.
    3. Biased composition libraries: Some libraries are inherently biased in their sequence composition. The most obvious example would be a library which has been treated with sodium bisulphite which will then have converted most of the cytosines @@ -80,6 +80,7 @@

      Common reasons for warnings

      only sequences which do not match. Sudden deviations in composition at the end of libraries which have undergone aggressive trimming are therefore likely to be spurious.
    4. +
    diff --git a/Help/3 Analysis Modules/6 Per Base N Content.html b/Help/3 Analysis Modules/6 Per Base N Content.html index 443a119..440b89a 100644 --- a/Help/3 Analysis Modules/6 Per Base N Content.html +++ b/Help/3 Analysis Modules/6 Per Base N Content.html @@ -13,7 +13,7 @@

    Per Base N Content

    Summary

    If a sequencer is unable to make a base call with sufficient confidence -then it will normally substitute an N rather than a conventional base] +then it will normally substitute an N rather than a conventional base call

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