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Currently only stranded data is supported. Some protocols will deliver reversely stranded data, we should add support for this.

Hi @t-neumann , I recently used Slam-Seq and we sequenced the results using Kappa Poly-A. We encountered the problem you have mentioned and got A>G increased instead of T>C on the Bluebee Analysis Pipeline. I transformed the FASTQ files using a FASTQ reverse complement in seqtk, explained here (https://www.biostars.org/p/364478/#364484) Do you have any recommendations for me? Any help would be appreciated.

Hi,

for the time being, I would advise you to simply reverse complement the reads as you have mentioned. However, I am not familiar with the Kappa Poly-A method - what does it give you? Reverse stranded reads or a mix of both stranded and reverse-stranded?

I just wanted to follow-up on this in case people are looking for an answer in the future with what we ended up doing to reverse complement the strands:

reformat.sh in=sample.fastq.gz out=sample_reverse.fastq.gz rcomp=t

Using this method, we were able to fix the problem mentioned above. For the record, Kappa Poly-A method is a stranded method and that is the reason we got the results we did.