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Old 04-27-2017, 01:49 AM   #1
ampa.aparicio
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Location: Barcelona

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Default Paired end fastq with very very different sizes between samples

Hello , I have received some paired end samples to analyze.
I'm new at all so, i don't know if it is normal but the R1 and R2 fastq for the same sample like 451 MB for the R1 and like 2.5 GB for the R2(both are uncompressed)
Do you think this is normal or may we have something wrong in the raw data?
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Old 04-27-2017, 03:53 AM   #2
GenoMax
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File sizes is never an accurate measure to compare datasets but the difference in this case seems significant. It is possible that you may have a corrupt file or two. It is also possible that this dataset may have been trimmed (for presence of adapters). Instead of using R1/R2 files together during trimming (as should be done) they may have been trimmed independently (not recommended).

I suggest that you use "repair.sh" from BBMap suite. You can thus re-sync files (so there are corresponding R1/R2 reads in cleaned files) and collect any singletons that may be present.
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