From Genome Analysis Wiki
Jump to navigationJump to search
21 bytes added
, 11:11, 4 September 2011
Line 35: |
Line 35: |
| | | |
| Although GC content can be calculated on fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command | | Although GC content can be calculated on fly each time, it is much more efficient to load a precomputed GC content from a file. To generate the file, use the following command |
− | qplot -r reference.fa -w windowSize -o reference.gc | + | qplot --rerefence reference.fa --windowsize windowSize --gc reference.gc |
| | | |
| ''Note'': Before running the qplot, it is critical to check how the chromosome numbers are coded. Some bam file use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from reference and dbsnp are consistent with the bam file.''' | | ''Note'': Before running the qplot, it is critical to check how the chromosome numbers are coded. Some bam file use just numbers, others use chr + numbers. '''You need to make sure that the chromosome numbers from reference and dbsnp are consistent with the bam file.''' |