Entering edit mode
6.3 years ago
Kenny
▴
30
Hi all,
I have a scaffold sequence and transcriptome. I am currently running GMAP to map and align the transcriptome to the scaffold genome. First step is to build a genome database. The first sequence ID is "scaffold_0_16608" and second is "scaffold_1_14918".
my command:
gmap_build -d oenopla_scaffold oenopla_rascaf_scaffold_121217.fa
Then I was checking the log file and I found something suspicious:
Reading coordinates from file /home/ktsang/.conda/envs/MyVirtualEnv/share/oenopla_scaffold.coords
Logging contig scaffold_0_16608 at scaffold_0_16608:1..16608 in genome oenopla_scaffold
=> primary (linear) chromosome
Logging contig scaffold_1_14918 at scaffold_1_14918:1..14918 in genome oenopla_scaffold
=> primary (linear) chromosome
Logging contig scaffold_2_14554 at scaffold_2_14554:1..14554 in genome oenopla_scaffold
=> primary (linear) chromosome
Logging contig scaffold_3_14024 at scaffold_3_14024:1..14024 in genome oenopla_scaffold
=> primary (linear) chromosome
I am guessing that the program count the scaffold_1_14918 as the first sequence because later "Writing contig scaffold_0_16608 to universal coordinates 812092889..812109496" looks weird to me.
Writing chromosome file /home/ktsang/.conda/envs/MyVirtualEnv/share/oenopla_scaffold/oenopla_scaffold.chromosome
Chromosome scaffold_1_14918 has universal coordinates 1..14918
Chromosome scaffold_2_14554 has universal coordinates 14919..29472
Chromosome scaffold_3_14024 has universal coordinates 29473..43496
...
...
Writing contig scaffold_0_16608 to universal coordinates 812092889..812109496
Writing contig scaffold_1_14918 to universal coordinates 1..14918
Writing contig scaffold_2_14554 to universal coordinates 14919..29472
Anyone with GMAP experience that can help explain this to me? Thanks!