Andrey Yurchenko

Dear Pasi, Thank you for the update. Is it relevant to the SeparateChromosome and JoinSinglesstoALL as well? Thanks! Andrey

Dear Pasi, During the working with OrderMarkers2 module, I found in my output that some individulas reombine much more than others, up to 12 times: Individual 16_3 ELT07977 recombines 1 times Individual 16_3 ELT07978 recombines 1 times Individual 16_3 ELT07980 recombines 1 times Individual 19_2 ELT08053 recombines 12 times Individual 19_2 ELT08055 recombines 8 times Individual 19_2 ELT08056 recombines 3 times Individual 19_2 ELT08057 recombines 2 times Individual 19_2 ELT08058 recombines 4 times...

Dear Pasi, I have carefully read the Lep-Map3 paper, but still, can not find some answers: 1) The default recombination1=0.001. What is the unit of recombination rate here? 0.001 recombination per CM per individual, per family or just a chance of recombination between two markers? How can it be adjusted for a vertebrate 1.5 GBp genome with 100 progeny and 40000 RAD-seq markers for example? 2) Could you please explain what the scale parameter is? If I use 100 - I have much more inferred recombination...

Dear Pasi, I have carefully read the Lep-Mpa3 paper, but still, can not find some answers: 1) The default recombination1=0.001. What is the unit of recombination rate here? 0.001 recombination per CM per individual, per family or just a chance of recombination between two markers? How can it be adjusted for a vertebrate 1.5 GBp genome with 100 progeny and 40000 RAD-seq markers for example? 2) Could you please explain what the scale parameter is? If I use 100 - I have much more inferred recombination...

I have carefully read the Lep-Mpa3 paper, but still, can not find some answers: 1) The default recombination1=0.001. What is the unit of recombination rate here? 0.001 recombination per CM per individual, per family or just a chance of recombination between two markers? How can it be adjusted for a vertebrate 1.5 GBp genome with 100 progeny and 40000 RAD-seq markers for example? 2) Could you please explain what the scale parameter is? If I use 100 - I have much more inferred recombination events,...

Dear Pasi, Another couple of questions for my case: 1) If I make unique mother - father pairs for half-sibs, should I or should not introduce a new family ID for these mother-fathers and halfsibs? Or should I leave the previous family ID for these familes? For example, a family 1 consists of mother1, father1, fahter2, offspring1, offspring2. Should I separate them into 2 familes with family1: mother1, father 1, offspring1 and family 2: mother 1, father2, ofspring2 Os it right logic? 2) Is it possible...

Hello, I use the last version of PBJelly and tried it on the example datset. I have got the error: 2017-06-30 15:34:53,048 [INFO] Running /export/home/aay2c/app2/PBSuite_15.8.24/bin/m4pie.py /export/home/aay2c/PROJECTS/zootoka/PBjelly/mapping/filtered_subreads.fastq.m4 /export/home/aay2c/PROJECTS/zootoka/PBjelly/reads/filtered_subreads.fastq /export/home/aay2c/PROJECTS/zootoka/PBjelly/lambda.fasta --nproc 23 -i 2017-06-30 15:34:53,107 [INFO] Extracting tails Traceback (most recent call last): File...

The same problem for me bowtie2-2.2.9/bowtie2-align-s: unrecognized option '--auto'