I got some Illumina Hiseq result in fastq files from my facility, but the yield is a lot lower than expected.
For example, the summary file for one sample shows that it contains 225566 +/- 0 clusters (PF), and I expected to get around 225566*32=7 million reads. But the fastq file only includes less than 0.5 million reads. One example read is
@HWI-1KL117_0134:6:2104:1422:2023#GNCAAT/1
NTTTTAATGAAAACACGGAAATTAAAAATTCTTGAAGGTGACATCCCTCCA
Because the sample has index barcode "GCCAAT", is it possible that the facility selected reads with bad barcode "GNCAAT" in stead of "GCCAAT" when demultiplexing? If it is true, is there anyway to rescue my sample?
Thanks in advance!
For example, the summary file for one sample shows that it contains 225566 +/- 0 clusters (PF), and I expected to get around 225566*32=7 million reads. But the fastq file only includes less than 0.5 million reads. One example read is
@HWI-1KL117_0134:6:2104:1422:2023#GNCAAT/1
NTTTTAATGAAAACACGGAAATTAAAAATTCTTGAAGGTGACATCCCTCCA
Because the sample has index barcode "GCCAAT", is it possible that the facility selected reads with bad barcode "GNCAAT" in stead of "GCCAAT" when demultiplexing? If it is true, is there anyway to rescue my sample?
Thanks in advance!
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