I am trying to understand how data that was uploaded to SRA (https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=4510743) can be analyzed with the assumption that the FASTQ file should contain replicate information (3 replicates within the sample). I downloaded the file and ran it with Nextflow, and it was mapped to the human genome and determined to contain unstranded reads of 50bp, both directions.
Which steps can I take to infer if the FASTQ file indeed is not demultiplexed?
Many thanks, Geo
The header of the FASTQ looks like this:
@SRR3467208.1 1/1 NTCTCTATGTCCACTCTGGAGCCTTTAAGTGCCACTTGAGGGCCTTTAAC + #4:D;DDEHHFHHIJJIJJGHGHJJI@HFIIJJHJJIG?9CFHIIIHHHG @SRR3467208.2 2/1 NGTGCTGTGTGTGCATGTGTGTGCGTGTGTGTGCTGTGCGTTTGTGTGTG + #1:B:BDDFFFFFFFBGFHIFIIFGFFGFGFGIIIIIIEFGGIIFFIFII @SRR3467208.3 3/1 NGTCACTTGGCATCTGGCCATCGGGCTGGATGCCGTGTTCCAGGCAGTAG + #1:A=DDDB<<CFAFGI@FGG9A@68CEG;DB?<DGGGE49?BBF2B=FF @SRR3467208.4 4/1 NTCCGGGGCTCCAGCAACCAGAAGAGGGAAAAGCTGTCTTCGGTGATGTC +