NCBI SRA sourced fastq data

In these FASTQ data:

  • The quality score identifier (+) is sometimes not a match for the sequence identifier (@).
  • The forward and reverse reads may be interlaced and need to be separated into distinct datasets.
  • Both may be present in a dataset. Correct the first, then the second, as explained below.
  • Format problems of any kind can cause tool failures and/or unexpected results.
  • Fix the problems before running any other tools (including FastQC, Fastq Groomer, or other QA tools)

For inconsistent sequence (@) and quality (+) identifiers

  • Correct the format by running the tool Replace Text in entire line with these options:

    • Find pattern: ^\+SRR.+
    • Replace with: +

Note: If the quality score line is named like “+ERR” instead (or other valid options), modify the pattern search to match.

For interlaced forward and reverse reads

Solution 1 (reads named /1 and /2)

  • Use the tool FASTQ de-interlacer on paired end reads

Solution 2 (reads named /1 and /2)

  • Create distinct datasets from an interlaced fastq dataset by running the tool Manipulate FASTQ reads on various attributes on the original dataset. It will run twice.

Note: The solution does NOT use the FASTQ Splitter tool. The data to be manipulated are interlaced sequences. This is different in format from data that are joined into a single sequence.

  • Use the Manipulate FASTQ settings to produce a dataset that contains the /1 reads**

    Match Reads

    • Match Reads by Name/Identifier
    • Identifier Match Type Regular Expression
    • Match by .+/2

    Manipulate Reads

    • Manipulate Reads by Miscellaneous Actions
    • Miscellaneous Manipulation Type Remove Read
  • Use these Manipulate FASTQ settings to produce a dataset that contains the /2 reads**

    • Exact same settings as above except for this change: Match by .+/1

Solution 3 (reads named /1 and /3)

  • Use the same operations as in Solution 2 above, except change the first Manipulate FASTQ query term to be:
  • Match by .+/3

Solution 4 (reads named without /N)

  • If your data has differently formatted sequence identifiers, the “Match by” expression from Solution 2 above can be modified to suit your identifiers.

Alternative identifiers such as:

@M00946:180:000000000-ANFB2:1:1107:14919:14410 1:N:0:1
@M00946:180:000000000-ANFB2:1:1107:14919:14410 2:N:0:1
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