I am using part of the same data that you used in your example which are coming from Denholtz_pcdhb19. The first 3 replications are ESC with 41 read length started with AAGCTT restriction enzyme. The other 3 replications are iPSC and in those i have problem because in 2 replications the read length is different than others and its 81bp. I dont know what fragment length to use in order to create a fasta file for mapping with reduce genome for mm10.
For those data we have primer with length 17 restriction enzyme 6 bp and barcode 2. The data starts with the restriction enzyme + contact .
I tried with different lengths (56,35,75) and with the 2 replicates with longer reads i get 0% in mapping.
What value to use for fragment length and what mapping parameters in order to be like your example?
Could you please help me with this issue ??
Hi
I am using part of the same data that you used in your example which are coming from Denholtz_pcdhb19. The first 3 replications are ESC with 41 read length started with AAGCTT restriction enzyme. The other 3 replications are iPSC and in those i have problem because in 2 replications the read length is different than others and its 81bp. I dont know what fragment length to use in order to create a fasta file for mapping with reduce genome for mm10. For those data we have primer with length 17 restriction enzyme 6 bp and barcode 2. The data starts with the restriction enzyme + contact . I tried with different lengths (56,35,75) and with the 2 replicates with longer reads i get 0% in mapping.
What value to use for fragment length and what mapping parameters in order to be like your example? Could you please help me with this issue ??
Best Dimitris