agshumate/Liftoff

Issue with mapping

genewlan opened this issue · 2 comments

genewlan commented

i use a gemome'gff document to map itself（reference=input）：
command as below:
liftoff -g in_genomic.gff -o in_genomic.gff3 -dir in_genomic -p 24 -chroms chr_pairs.txt -u in_genomic_unmapped -exclude_partial in_genomic.fas in_genomic.fas
next, I compered the in_genomic.gff and in_genomic.gff3.

the mapping result:
in_genomic.gff, size:18M; (origin),100000lines
in_genomic.gff3, size:10M; (mapping), 60000lines
there are 10000 lines ummapped
why is there so big difference.

i want to ask where is the problem，the command lines or the parameter？
the version of liftoff is 1.6.3

agshumate commented

are there features other than genes/transcripts/exons in your gff file?

genewlan commented

NO, nothing more.
I compared the origin .gff profile with the mapping some genes was missed in the mapping profile.
what I used the assembly number is GCA_900073075.1 that you can download at https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/073/075/GCA_900073075.1_CML3066.v2/

my OS is ubantu 20.4
the version of liftoff is 1.6.3