Partek Flow Documentation

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The task allows user to trim reads in different ways (Figure 1), including:

  • Trim bases based on quality score
  • Trim bases from 3'-end
  • Trim bases from 5'-end
  • Trim bases from both ends


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SubtitleTextSelect a Trim

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mode to trim poor quality bases from reads
AnchorNameTrim bases modes

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Trim bases from 5'-or 3'-end (Figures 12-23) allows a fixed number of bases to be trimmed away from the 5'- or 3'-end of the reads. These two functions are useful for when your read length is constant. This is not recommended if the read length is not constant, since good quality bases from shorter reads are likely trimmed away by these functions.

 


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SubtitleTextTrim bases from 5'-end
AnchorNameTrim bases

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SubtitleTextTrim bases from 3'-end
AnchorNameTrim bases 3'-end

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Trim bases from both ends (Figure 34) allows user to keep only bases from a fixed start and end position of the reads. This is particularly useful if poor quality bases are observed on both ends  of the read. So instead of performing trim bases successively from the 5'- and 3'-end, the trim bases will only be performed once by trimming from both ends.

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SubtitleTextTrim bases from both ends
AnchorNametrim-both-ends

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Trim bases based on quality score (Figure

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5) is probably the most useful function to trim poor quality bases from the 5'- or 3'-ends of reads. This function allows dynamic trimming of bases depending on quality score. The trimming can be done from either 5'-end, 3'-end or both ends of the reads. The function evaluates each base from the end of the read and trims it away until the last base has a quality score greater than the specified threshold. For an extensive evaluation of read trimming effects on Illumina NGS data analysis, see Del Fabbro et. al. [1]. 


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SubtitleTextTrim bases based on quality score
AnchorNametrim-qual-score

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Advanced options

In some cases, the reads that result from base trimming can have very short read lengths and thus are not recommended for alignment. Thus, Partek® Flow® Flow provides the option to set a Min read length after base trimming. This discards reads that are shorter than the set length. 

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The Quality encoding option refers to the Phred quality score encoded within the FASTQ input file. The list of available options are: Phred+33Phred+64Solexa+64 and Integers. Selecting Auto-detect will determine whether the quality encoding is Phred+33 or Phred+64. For Solexa data, you will need to select Solexa+64. For most of datasets, auto-detect option works very well with a few exception cases where the base quality score falls into the grey zone (ambiguous zone) of Phred+33 and Phred+64 score. However, if the quality-encoding scheme is known, we recommend to selecting the encoding format directly from the quality encoding list.

Figure 5 6 shows the options available for all the different selection of Trim bases function. Note the default Min read length is 25bp. For micro RNA sequencing data, this default Min read length needs to be set to a smaller value (we recommend 15) to account for mature microRNAs.

 


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SubtitleTextTrim bases options. A) Trim from 3'-end; B) Trim from 5'-end; C) Trim from both ends; D) Trim based on base quality score
AnchorNametrim-advanced

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Trim Bases Task Details Page

The Task Details page for Trim bases can be accessed by selecting the task node Trim bases, and subsequently selecting Task Details from the Task results section. In the Task details page, several sections are available:

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  • Command Lines: shows the commands used for running Trim bases function by the software Partek Flow

Trim Bases Task Report Page

The Trim bases Task Report page can be accessed by selecting either the Trim bases task node or Trimmed reads data node and then selecting the Task Report from the Task results section of the context sensitive menu. There is a link at the bottom of the page to directly go to the Task Details page. The page displays the following components:

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  • Average base quality score per position of trimmed reads: shows the average base quality score at each position of the trimmed reads for all samples in the project.

Trim Bases Output Files

The Trim bases function produces trimmed unaligned reads which is named as Trimmed Reads data node. The Trimmed Reads node will have the "trimmed" word appended to the filename. The Trimmed Reads data can be downloaded by selecting the Trimmed Reads node and then select Download data from the context sensitive menu. However, if you have access to the Partek Flow server, you can go to the Task Details page and identify the location of the output files from the Output Files section as described on the Trim Bases Task Details section above. The Trimmed Reads data node will have the same format as the raw data.

References

  1. Del Fabbro C, Scalabrin S, Moragante M, Giorgi FM. An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS ONE. 2013; 8(12): e85024.

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