Hi,
I gave few samples for shotgun metagenomics sequencing. The company sequenced them but I have a doubt regarding the read file or fastq files they have provided to me.
1. It is a paired end sequencing and there are on average 240,000+240,000 (Forward+Reverse) reads for each sample. Which I think is way too less than expected. Normally Miseq platform should provide at least 10-20 million reads per run for each sample? The extracted DNA had average concentration of aprrox. 80ng/microLitre?
Can anyone explain me what might be the problem? Was it problem with the sample or sequencing?
How many samples did you sequence? Output depends on many factor like number of samples, kit used, time etc. This expecting 10-20 million reads per samples as universal does not make much logic. https://www.illumina.com/systems/sequencing-platforms/miseq/specifications.html
Abhijeet Singh Thanks for your response. We had 10 samples in total. I am not aware about the reagents and kits they used.
I think most sequencing companies can give you the choice to opt for higher number of reads for a higher price, as they will be using more reagents per sample and decrease multiplexing for those sequencing runs. There should also be a specified (higher) cutoff value of DNA concentration for those more demanding sequencing projects.
- Badges
- Science topic
- Similar topics
- Cognitive Science
- Thinking