keyerror

[Hemaprasanth24]

Good afternoon, Myself hemaprasanth iam encountering a key error while comparing 2 chromosomes

(major_project) hema@hema-Aspire-A715-51G:~/major_project$ syri -c /home/hema/major_project/sam_file/Human_mouse/human_mouse_ch10/human_ch10_mouse_ch3.sam -r /home/hema/major_project/Fasta_files/GRCh38/GRCh38_ch10.fasta -q /home/hema/major_project/Fasta_files/GRCm39/GRCm38_ch3.fasta -k -F S --dir /home/hema/major_project/syri_output/human_mouse_ch10/human_ch10_mouse_ch3 --prefix human_ch10_mouse_ch3 Reading Coords - WARNING - Chromosomes IDs do not match. Reading Coords - WARNING - Matching them automatically. For each reference genome, most similar query genome will be selected. Check mapids.txt for mapping used. Reading Coords - WARNING - Reference chromosome NC_000010.11 do not have any directed alignments with its homologous chromosome in the query genome (NC_000069.7). Filtering out all corresponding alignments. Traceback (most recent call last): File "/home/hema/anaconda3/envs/major_project/bin/syri", line 6, in main(sys.argv[1:]) File "/home/hema/anaconda3/envs/major_project/lib/python3.8/site-packages/syri/scripts/syri.py", line 326, in main syri(args) File "/home/hema/anaconda3/envs/major_project/lib/python3.8/site-packages/syri/scripts/syri.py", line 183, in syri if len(seq) < bchr_size[chrlink[chrid]]: KeyError: 'NC_000010.11'

[mnshgl0110]

Are you comparing only Human-Chr10 vs Mouse-Chr03 ? If so, are these chromosomes homologous to each other? Syri, needs homologous chromosomes as it needs to find synteny. Check the documentation here: https://schneebergerlab.github.io/syri/

[Hemaprasanth24]

Good morning, Thanks for the replay actually I am try to identify variants between human and mouse actually the gene location between human and mouse differs so i decided the compare like this such as human-chr10 vs mouse-chr01 human-chr10 vs mouse-chr02 human-chr10 vs mouse-chr03 human-chr10 vs mouse-chr04 . . . human-chr10 vs mouse-chr0Y

[mnshgl0110]

I do not think this would work as syri requires homologous chromosomes. Please check the documentation.