Entering edit mode
3.1 years ago
Futuremaking
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I have sequenced a few samples using hiseq4000 at Novogene. Standard output size is expected to be at least 150G/lane. I got only ~70G. Novogene's explanation was that something might be wrong with the reagents. Instead of repeating the whole run, Novogene only agreed to run another 60G using lane sharing on Novaseq 6000. They said you can used the previous run plus these new reads to do data analysis. I don't even know how to combine the two FASTQ files. Can anyone suggest any codes for combining the files?
This is a bit of bait for stories of the kind: Grandma always told me: "Boy, listen to me, if you buy cheap, you buy twice.". But unfortunately, 1. grandma didn't know about sequencing companies, 2. buying expensive was no guarantee either. I think the only lesson to take here is not to pay the crafts-person (that's what they are essentially) before the work is flawless, and never pay upfront.
If the two runs are not equal length then you would want to trim one of them down to the same length before doing any combining. It is possible to simply
catthe relevant files (both R1 and R2's together in the same order) for two runs to create a larger file.One could also align them separately and then merge the bam-files with samtools merge as technical replicates.
Thanks! Illumina's tech support just used Copy Run1 + Run2 .\Combined using command line. It seems working okay as the total size matches with Run1+Run2. Do I still need to try cat?
Was that done on windows?
catwas if you were working on Linux. So you should be all set if you followed Illumina's instructions.