New guy here, hope these aren't stupid questions.
I have a whole bunch of fq.gz files I've been provided with. I need to use them along with their associated BAMs to run CNVnator. I've been reading a bunch of tutorials on using CNVnator and trying out some scripts and am wondering whether:
- Will I need to untar the fq.gz files for CNVnator to use them?
- Will I need to convert the fq to fa files?
- Will I need to split the two large fa files into individual scaffold fa files for CNVnator to work properly?
I've run CNVnator already, using the fq.gz files, and it has produced a histogram - but it doesn't look like the examples I see elsewhere. Here is a bit of it:
deletion scaffold00002:34001-43000 9000 0 1.77081e-11 3.27327e-82 9.107e-09 5.30333e-62 1 deletion scaffold00002:50001-55000 5000 0 0.00025541 8.59242e-42 9.71095 1.39214e-21 1 deletion scaffold00002:66001-75000 9000 0.0355466 0.000366838 8.52037e-38 9.107e-09 5.30333e-62 1 deletion scaffold00005:53001-57000 4000 0 0.0469971 1.0937e-31 2521.11 1.77201e-11 1 deletion scaffold00005:113001-116000 3000 0.00260097 2.16931 3.69832e-21 1 1 1 deletion scaffold00005:183001-185000 2000 0.00780292 2540.93 6.48799e-11 1 1 1
It lacks the headings and is formatted somewhat differently to the examples I've looked at. Has it not worked correctly?
My code was:
cnvnator -root WN-8.root -tree /gpfs/projects/p-orsinil01/CNVandT/bwa_mapping/WN-8.bam > WN-8_extract.out cnvnator -root WN-8.root -his 1000 -d /gpfs/nbu/pxo289/bin/CNVnator/CNVnator_v0.3.2/src > WN-8_histogram.out cnvnator -root WN-8.root -stat 1000 > WN-8_stats.out cnvnator -root WN-8.root -partition 1000 > WN-8_partition.out cnvnator -root WN-8.root -call 1000 > WN-8_calls.out
Any help is appreciated.