Frequently Asked Questions (FAQ)

- When loading the reference genome sequence in FANSe program, it shows an error message “Out of memory” or “Stack overflow”.

This problem most likely appears when you run the FANSe program in a 32-bit system and try to use a reference genome larger than 400Mb. If this error constantly appears please switch to 64-bit system, or perform the mapping chromosome by chromosome, since the current FANSe does not stably process multiple chromosomes.
Another reported possibility is that the reference genome file is not in FASTA format.

当在FANSe程序中加载参考基因组序列的时候,出现一条错误信息"out of memory"或"stack overflow"


- I bought the newest hexa-core CPU, however FANSe uses only one core. Is it possible to accelerate the mapping by using all cores?

For stability we do not offer multithreading option currently in version 7.2. Nevertheless you can start several instances of FANSe to map different datasets or chromosomes simultaneously in one computer if you have enough RAM. In our test, 8GB RAM is sufficient for 7 instances of FANSe to map reads to human chromosome 1 in parallel with almost linear performance increase on an 8-core workstation. Moreover, we are working on a novel technical strategy of efficient parallelization to unleash the power of 24-core or 48-core workstation with limited memory and this feature will be added (hopefully) in the next major version of FANSe.

The new generation of FANSe2 supports unlimited parallelization. Please try it out.




- Do I need to use the “masked” genome? When should I use it?

For RNA-seq applications, masked genome is highly recommended. A read map to the repetitive region will be mapped to the whole genome many times, making it impossible to estimate its location. Using masked genome also accelerates the mapping process significantly.
For DNA sequencing applications, e.g. resequencing and methylation analysis, you may use non-masked genome if you are interested also in the repetitive sequence when you have long reads.

我需要使用被遮罩基因组(masked genome)吗?我什么时候该使用它?


- My reference genome is not large, containing 16 chromosomes. However the chromosome number in the FANSe result file seems not fully correct. What should I do?

The current FANSe version may make mistakes when exporting the chromosome number in some cases with multiple chromosomes, although the mapping itself is correct. Therefore we recommend you to do the mapping once a chromosome. Alternatively, you can make a program to join all the chromosomes into one entire string as the reference sequence and perform the mapping. We are trying to solve this problem and this bug will be fixed in the next version.

FANSe2 corrected this bug and fully supports multiple chromosomes.



新的 FANSe2 算法已发布,完美支持多染色体的比对。请您使用新的FANSe2


Operated by Institute of Life and Health Engineering, Jinan University
Copyright (c) 2011-2012 All rights reserved