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4.9 years ago
liu9827885
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0
Hi, I'm new for WGS. And there were some problems about the reads of different sequencing platform. One sample were sequenced by the illumina with PE150. Meanwhile, it was used to sequence by the BGI with PE100. I'm not sure could I combine the bam of the two different reads after bwa-mem and sort ? Because they have the same base quality standard. Thanks a lot !
Illumina is a company that offers multiple sequencing platforms so
by the Illuminais not informative.BGI is a service provides. You should find out 1) on which platform (HiSeq, NExtseq, Novaseq...) the first and second sample have been sequenced. If thes platforms are similar probably merging is ok.Alternatively, call variants on both datasets and only take reproducable variants for downstream analysis.Thanks for your reply. I check the platform of illumina and bgi is HiSeq-2500 and BEGISEQ-500. But the different length of PE can merge directly?
You could merge it but I wouldn't unless I had a very good reason to do so. Both are radically different seq technologies. There have been a number of comparisons which show they are quite similar, but you'll still find some issues around different protocols eg amplification biases, different TAs, software eg base callers and so on. They will each deal with certain motifs differently.
If you can, I would call SNVs on each using the same methods and use each of them as technical variates, both of which are not able to detect the true biological variation 100% accurately.
Oh, and @ATpoint - BGI and MGI sequencers do exist these days (BGI is not just a service provider). Apparently costs are about 50% of Illumina, which makes for some welcome competition.
Ok, did not know that, my bad.