Downloaded fastq from SRA, am I right in thinking it isn't interleaved paired-end reads?
Downloaded fastq from SRA using fasterq-dump I used grep on a sequence identifier I pulled using head:
grep HWI-ST808:122:C1B50ACXX:2:1101:2426:2231 C1_p_K4me3.fastq
output:
@SRR1035416.1 HWI-ST808:122:C1B50ACXX:2:1101:2426:2231 length=51
+SRR1035416.1 HWI-ST808:122:C1B50ACXX:2:1101:2426:2231 length=51
If anyone can take a second to confirm that I have unpaired reads that would be amazing. Thank you for your time!!
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GenoMax
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jennxyzhang •
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jennxyzhang •
1 answer
This looks like a single-end dataset. So no, those are not "interleaved" reads. In older fastq files entire fastq header was repeated after the + separator in line 3 of a fastq record. That is what you are observing.
Edit: This dataset is from 2013.
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