MCScanX truncated results.
koushik1989 opened this issue · 4 comments
Dear developer and users, I am facing an issue while running MCScanX between two very closely related Drosophila species. I used blastp to blast proteins of each genome with itself and the target genome using " blastp -query -db -evalue 1e-10 -max_target_seqs 5 -outfmt 6 " and concatenated all 4 outputs generated using cat cmd. I concatenated the .gff from two genomes and ran MCScanX. The run completes without any errors but the collinearity file is incomplete with only 3 alignments. I have attached the output with this query. Kindly suggest where am I going wrong. I expect a high degree of collinearity between the genomes as they are sibling species. My inputs are in following formats.
I tried running blastall with the same protein files only to find the collinearity file with only 1 alignment.
$ head Dnas_Dalb_mcscanX.blast
XP_034100989.1 XP_034100989.1 100.000 18460 0 0 1 18460 1 18460 0.0 36057
XP_034100989.1 XP_034104103.1 27.285 1444 753 60 114 1461 195 1437 8.20e-67 255
XP_034100989.1 XP_034104103.1 27.795 1324 716 59 229 1461 148 1322 9.48e-64 245
XP_034100989.1 XP_034104103.1 29.673 1102 575 63 110 1172 420 1360 4.33e-60 233
XP_034100989.1 XP_034104103.1 26.980 745 362 32 90 697 738 1437 5.19e-36 153
$ head Dnas_Dalb_mcscanX.gff
NC_047628.1 XP_034099297.1 24519288 24535641
NC_047628.1 XP_034100555.1 24538132 24554148
NC_047628.1 XP_034100562.1 24623105 24626154
NC_047628.1 XP_034099816.1 24628513 24629322
NC_047628.1 XP_034097326.1 24633653 24637715
collinearity_file.txt
Looking forward for a positive response.
thank you
I have solved the issue thank you.
Dear Koeshik1989, I am experiencing the same problem. How exactly did you fix this? Best regards.
Can someone post a solution to this problem here? @koushik1989 @thesnakeguy