Question: Handling a compressed fastq file in CNVnator
gravatar for whyaretherehiddenwells
4.2 years ago by

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.

open cnvnator fasta • 1.2k views
ADD COMMENTlink modified 4.2 years ago by RamRS26k • written 4.2 years ago by whyaretherehiddenwells0
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