Is interleaved Fastq files the same as interlaced fastq
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10 weeks ago
RCMC • 0

There are errors in BWA-MEM2 that there

fastq • 555 views
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Sorry I accidentally hit enter

BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to combine it to a single file and hoping to fix it

However, I am confused if the interlaced and interleaved fastq are the same since SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq

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SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq

Both programs will accept separate paired-end files. The reads in the files do need to be in exact same order (in sync) as noted by rpolicastro .

SPAdes seems to refer to interleaved data as interlaced.

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No need to post a comment, you can just edit your original post after the fact

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Interleaved is the standard term; SPAdes calls them interlaced. As rpolicastro stated, your reads may have become disordered.

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This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse reads in both files. I would try running them through seqkit pair first to try and fix them.

Even better would be to figure out what step prior to this could have caused it and remediate the problem at the source. If there were any trimming or filtering steps I would start there.

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