Dear Andreas,
I have been using Lofreq with a set of data from bacteria to identify low frequence SNP that explain microevolution. I wanted to filter by AF lower than 95% and above 75% to generate a smaller file to work with. There is any way I can do it with lofreq call?
Thanks,
Elena
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
filtering is a separate downstream step. You will have to run 'lofreq
filter' with '--af-min 0.75 --af-max 0.95' to apply the mentioned
allele frequency filtering criteria.
For older versions (i.e. <2) you would use 'lofreq_filter.py
--min-freq' but there's no direct equivalent for maximum allele
frequency.
Dear Andreas,
I have been using Lofreq with a set of data from bacteria to identify low
frequence SNP that explain microevolution. I wanted to filter by AF lower
than 95% and above 75% to generate a smaller file to work with. There is any
way I can do it with lofreq call?
Thanks,
It have the beta version and was not working but I download the last
version of lofreq and it works perfectly.
Thanks also for improving the information in the help file.
filtering is a separate downstream step. You will have to run 'lofreq
filter' with '--af-min 0.75 --af-max 0.95' to apply the mentioned
allele frequency filtering criteria.
For older versions (i.e. <2) you would use 'lofreq_filter.py
--min-freq' but there's no direct equivalent for maximum allele
frequency.
Hope this helps,
Andreas
On 22 May 2014 14:16, Elena marulin@users.sf.net wrote:
Dear Andreas,
I have been using Lofreq with a set of data from bacteria to identify low
frequence SNP that explain microevolution. I wanted to filter by AF lower
than 95% and above 75% to generate a smaller file to work with. There is
any
way I can do it with lofreq call?
Thanks,
It have the beta version and was not working but I download the last
version of lofreq and it works perfectly.
Thanks also for improving the information in the help file.
Kindly,
Elena
2014-05-22 20:04 GMT+10:00 Andreas Wilm onde@users.sf.net:
Hi Elena,
filtering is a separate downstream step. You will have to run 'lofreq
filter' with '--af-min 0.75 --af-max 0.95' to apply the mentioned
allele frequency filtering criteria.
For older versions (i.e. <2) you would use 'lofreq_filter.py
--min-freq' but there's no direct equivalent for maximum allele
frequency.
Hope this helps,
Andreas
On 22 May 2014 14:16, Elena marulin@users.sf.net wrote:
Dear Andreas,
I have been using Lofreq with a set of data from bacteria to identify low
frequence SNP that explain microevolution. I wanted to filter by AF lower
than 95% and above 75% to generate a smaller file to work with. There is
any
way I can do it with lofreq call?
Thanks,
Dear Andreas,
I have been using Lofreq with a set of data from bacteria to identify low frequence SNP that explain microevolution. I wanted to filter by AF lower than 95% and above 75% to generate a smaller file to work with. There is any way I can do it with lofreq call?
Thanks,
Elena
Hi Elena,
filtering is a separate downstream step. You will have to run 'lofreq
filter' with '--af-min 0.75 --af-max 0.95' to apply the mentioned
allele frequency filtering criteria.
For older versions (i.e. <2) you would use 'lofreq_filter.py
--min-freq' but there's no direct equivalent for maximum allele
frequency.
Hope this helps,
Andreas
On 22 May 2014 14:16, Elena marulin@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
Hi Andrea,
It have the beta version and was not working but I download the last
version of lofreq and it works perfectly.
Thanks also for improving the information in the help file.
Kindly,
Elena
2014-05-22 20:04 GMT+10:00 Andreas Wilm onde@users.sf.net:
Hi Elena,
I just noticeda few more tiny errors in the usage information and
fixed them. Do let me know if you have any ideas for improvement or
find flaws.
Thanks and good luck with your analysis,
Andreas
On 23 May 2014 08:35, Elena marulin@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC