Question: FASTQ file split (forward and reverse not of same length)
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gravatar for galaxyNewbie
6 months ago by
galaxyNewbie30
galaxyNewbie30 wrote:

Is there a Galaxy package which will split a previously joined fastq which will have unequal forward and reverse lengths? FastqSplitter and similar Galaxy packages all require that the length be the same for the package to split correctly, but mine with have unequal lengths.

Thank you.

merge fastq trim join split • 328 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by galaxyNewbie30
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gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

You need to obtain the original read datasets (before joined). The FASTQ joiner/splitter tools are designed to work with reads of the same length only.

Or, as a potential workaround, and if you know the read lengths and they are not variable, you could try the tool NGS: QC and manipulation > Trim sequences. Run it twice on the original dataset. You'll be removing 3' ends, to create a 5' (forward reads) dataset and then the reverse.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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