Closed huguanjing closed 4 years ago
Hi,
The readinfo.txt file looks fine. What is the content of A2-10-R1.A.vs.D.txt?
The A2-10-R1.A.vs.D.list file would be generated with the next command, running eagle-rc.
In your case it would be: eagle-rc -a A2-10-R1.refsort.bam -o A2-10-R1.A.vs.D -v A2-10-R1.A.vs.D.txt \ A2-10-R1.A.vs.D.readinfo.txt > A2-10-R1.A.vs.D.list
Did you run this step?
Thank you for the speedy response! I tried both eagle and eagle-rc scripts again and they worked. It turned out my original job was somehow killed halfway so it didn't output 'A2-10-R1.A.vs.D.txt'. Thanks again!
Hi @tony-kuo! I followed the
tetraploid_analysis.sh
to prepare vcf and run Star mapping. When it came to the EAGLE step running below script, the run finished but output is empty. Would you please help me to trouble shoot? Thanks a lot!