After sequencing my samples, I needed to convert my files (Fastq) to BAM files because I want it to be viewed on IGV. This lead to reanalysing the files on Illumina Next Seq. Afterwards, I found out that I have a lot of undetermined reads in the fastq files and the number of reads in the BAM files are just too little to be true and nothing could be seen when the files are opened. Note that the initial Fastq file size was much bigger. I suspect a demultiplex problem but I don't know how to go about solving it. Any suggestion would be highly appreciated...
You are describing the problem but you did not provide any information why and how you did, what you did.
I would suspect that you already have demultiplexed samples since demultiplexing of samples is most commonly done at the instrument level in a sequencing facilities.
Abhijeet Singh Yes, it's done at instrument level and I was able to demultiplex the samples by reanalysing the run again. Thankyou!
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