Faridul Islam

Dear Pasi, Thanks for your reply. I was waiting for your suggestions. Your reply clarified most of my confusion except the last issue regarding thinning sequencing data. Could you suggest any tool by which I can make specific window bin size and select one makers from that window bin or I need to create my own bash script for that purpose? Your suggestion would be highly appreciated. Best Regards, Farid

Dear Pasi, Today I got a couple of issues to discuss, and I could also use some advice on another issues. First of all, I ran into a weird thing with the "removeNonInformative" argument. Since it works in both ParentCall2 and Filtering2 modules, I tried it out in two ways: 1. Option-1: I used "removeNonInformative" argument in ParentCall2 module, then Filtering2 module with dataTolerance=0.001 argument . 2. Option-2: I used both "removeNonInformative" and dataTolerance=0.001 argument in Filtering2...

Dear Pasi, Thanks for the info! I'll let you know if I run into any problems. Seriously, this tool you built is awesome! It makes dealing with giant mapping datasets so much easier. Hope Jesi was able to fix the issue! Good luck to Jesi too. Best regards, Farid

Dear Pasi, We previously addressed an issue with the Filtering2 command in another thread. Today, I'd like to discuss a different topic related to linkage map generation. I have access to the reference genome for the plant I'm studying, which was used for SNP calling. Since I know the physical position of the markers, I want to create a linkage map based on this known order. On the Wiki page, I found the following command: java -cp bin/ OrderMarkers2 evaluateOrder=order2.txt data=data_f.call improveOrder=0...

Dear Pasi, Thanks for your reply! You were right about the end-of-line issue. I ran the same command and data in the Linux environment within Windows (WSL2), and it worked successfully. Out of curiosity, like I mentioned earlier, ParentCall2 was able to read my data and generate a "CALL File." However, Filtering2 couldn't read this same "CALL File." This makes it seem like ParentCall2 might not be creating a correct "CALL File." Interestingly, in the Linux system, Filtering2 had no problem reading...

Dear Pasi, I just started using Lep-MAP3 (v. 0.5) for linkage map construction for F2 self-crossed tomato population. ParentCall2 successfully read my data and saved the data for next stage. I did not use the "removeNonInformative=1" options when running ParentCall2. Here is the ParentCall2command I used: java -cp .\bin\ ParentCall2 data=tomato_F2_pedigree.txt vcfFile=format_2_final_for_mapping.vcf >t_data_p.call However, I encountered Error:504 when running Filtering2 with "dataTolerance=NUM" and...