Hi
I'd like input with regards to how a mixture of data would behave for exom seq samples.
So, the set up is this. Straight forward, 2*101 bp HiSeq2000 runs on whole exom seq Illumina truseq samples. We have however had some (quite a lot of) issues in the lab and with the HiSeq. Not to mention that the computer crashed as well during one run. So after three runs we now have 1*101 bp (read2) and 101+80bps from 40 samples as well as 2*101bp from another 40 samples.
So my question is whether you guys think it could be ok to align the 2*101 and the 101+80, bwa paired end way and the 101 bp from read 2 separately and then merge the bams. This would give me:
40 samples, straight 2*101 bp aligned data.
40 samples, 101 + 80bp paired end aligned plus 101 bp single read aligned.
Thoughts? Pitfalls to be avoided? There's a nice que on the system so I'd really like to avoid having to wait for a rerun.
I'd like input with regards to how a mixture of data would behave for exom seq samples.
So, the set up is this. Straight forward, 2*101 bp HiSeq2000 runs on whole exom seq Illumina truseq samples. We have however had some (quite a lot of) issues in the lab and with the HiSeq. Not to mention that the computer crashed as well during one run. So after three runs we now have 1*101 bp (read2) and 101+80bps from 40 samples as well as 2*101bp from another 40 samples.
So my question is whether you guys think it could be ok to align the 2*101 and the 101+80, bwa paired end way and the 101 bp from read 2 separately and then merge the bams. This would give me:
40 samples, straight 2*101 bp aligned data.
40 samples, 101 + 80bp paired end aligned plus 101 bp single read aligned.
Thoughts? Pitfalls to be avoided? There's a nice que on the system so I'd really like to avoid having to wait for a rerun.