Question: Combining fastq/sorted sam files from same libraries run on HiSeq and NextSeq
0
gravatar for senowinski
9 weeks ago by
senowinski10
European Union
senowinski10 wrote:

Can I combine fastq/sorted sam files from the same samples and same libraries that were run on both the HiSeq and NextSeq? If it is absolutely fine (are there any pitfalls?), is there anything I should be weary of? Thanks!

sequencing next-gen • 156 views
ADD COMMENTlink modified 9 weeks ago by Devon Ryan73k • written 9 weeks ago by senowinski10

What do you want to do with them? Are you doing variant calling or something else?

ADD REPLYlink written 9 weeks ago by Devon Ryan73k

I want to call copy number variations on them. I should also add, this is low-pass sequencing combined depth of coverage will be 0.2X. thanks

ADD REPLYlink written 9 weeks ago by senowinski10
1
gravatar for Devon Ryan
9 weeks ago by
Devon Ryan73k
Freiburg, Germany
Devon Ryan73k wrote:

If you're doing CNV detection then just merge the files and call it done. If you were doing something like variant detection or methylation sequencing then maybe you'd want to treat things a bit differently (due to the different error profile in the two aligners), but that's not needed in this case.

ADD COMMENTlink written 9 weeks ago by Devon Ryan73k
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