Question: Combining fastq/sorted sam files from same libraries run on HiSeq and NextSeq
0
gravatar for senowinski
2.1 years ago by
senowinski30
European Union
senowinski30 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 • 553 views
ADD COMMENTlink modified 2.1 years ago by Devon Ryan92k • written 2.1 years ago by senowinski30

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

ADD REPLYlink written 2.1 years ago by Devon Ryan92k

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 2.1 years ago by senowinski30
1
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k 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 2.1 years ago by Devon Ryan92k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2120 users visited in the last hour