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Old 04-08-2018, 10:27 AM   #1
bong28
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Default Number of reads in paired end fastq files

I have two fastq files from paired end sequencing. I got those two files after converting a bam file to fastq. I was doing a quality check on the files, when I saw the number of sequences option in FASTQC tool gave different number for both files.
The number of sequences for read 1 was : 508168252
The number of sequences for read 2 was : 512336921

Shouldn't this be the same?
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Old 04-08-2018, 01:57 PM   #2
GenoMax
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Normally yes.

I suggest that you use use "repair.sh" from BBMap suite to re-pair the reads and remove singletons to a separate file. Assuming your conversion has properly worked.
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Old 04-08-2018, 10:53 PM   #3
bong28
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Thanks for your reply

Last edited by bong28; 04-08-2018 at 11:38 PM.
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