A few days back we initiated sequencing run for multiplexed exome samples in HiSeq2500 platform. Due to human error cluster generation for reverse reads finished up as a disaster. So we will be having BCL files only for forward reads. Is it ok to consider forward reads for downstream analysis. Will it create any problem while doing bcl to fastq conversion step. Please share views if anybody encountered similar situation.
I agree with Peter, I think you should use it but strand biased sequencing errors will be impossible to detect.
If the sequencing facility messed things up, you should hold them accountable and get things resequenced, that is what we do when things go wrong. I agree, single end is adequate for numerous applications, so it depends what you are doing with this data. Good luck :).
Exome samples are from familial cases. Samples of 4 affected member from each family has gone for sequencing. Anyways re-sequencing has already initiated with same strategy. Hopefully this time nothing will go wrong, My primary question still is whether I can convert the bcl files forward reads from the incomplete run data using CASAVA or some other softwares.
You can use the Bcl2fastQ tool and you need to workout with the sample sheet as you have only one tag read. Use only version 1.6 or 1.8 as 2.0 is only for NextSeq. You can use 1.8.4 version for HiSeq
best regards
Surendra K Chikara
Thanks all for your valuable comments. Now, I want to extend my question.
What are the differences one might expect while analyzing reads coming out from single-end sequencing against forward reads from paired-end sequencing.
In a clear way, what if I consider forward reads from this paired-end sequencing as a single-end sequencing experiment.
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