SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 8 of 8
Search took 0.00 seconds.
Search: Posts Made By: netasha
Forum: Bioinformatics 07-15-2017, 07:44 AM
Replies: 347
Views: 185,363
Posted By netasha
Hi Brian, I have updated the bbtools to the...

Hi Brian,

I have updated the bbtools to the most recent version and switched to bbduk.sh.

I was trying to use the mink to ask for a subset of k-mer for trimming. However, once I added the...
Forum: Bioinformatics 07-14-2017, 01:08 PM
Replies: 347
Views: 185,363
Posted By netasha
Thanks for your detailed explanation. Those are...

Thanks for your detailed explanation.
Those are really good suggestions and I will definitely take it! Thank you so much!
Forum: Bioinformatics 07-14-2017, 11:02 AM
Replies: 347
Views: 185,363
Posted By netasha
Sounds reasonable. Then I will stay with bbduk. ...

Sounds reasonable. Then I will stay with bbduk.

As for quality-trimming, if I ask for bases below q20 from both left and right end will be trimmed, how do you define left end and right end for a...
Forum: Bioinformatics 07-14-2017, 09:43 AM
Replies: 347
Views: 185,363
Posted By netasha
Thanks for your reply. Good to know that has been...

Thanks for your reply. Good to know that has been fixed! The version I used is BBDuk2 version 36.71.

A similar question is:
If I set up the following three parameters:
1)...
Forum: Bioinformatics 07-14-2017, 07:41 AM
Replies: 347
Views: 185,363
Posted By netasha
Hi Brian, I have questions on the parameter...

Hi Brian,

I have questions on the parameter setting for bbduk2.sh.

I found that when I set both K-mer trimming and minlength and maxlength, for the input reads, if they don't contain the...
Forum: Bioinformatics 02-02-2017, 09:42 AM
Replies: 347
Views: 185,363
Posted By netasha
That's why I was looking for a parameter which...

That's why I was looking for a parameter which can restrict this short 3mer to be anchored at the rightmost position. I thought you provided such parameters already: restrictright=3. Am I right?
...
Forum: Bioinformatics 02-02-2017, 07:16 AM
Replies: 347
Views: 185,363
Posted By netasha
Thanks for your quick reply! I was thinking...

Thanks for your quick reply!
I was thinking doing it sequentially as well. But what is the "ktrimexclusive"?
Forum: Bioinformatics 02-02-2017, 06:53 AM
Replies: 347
Views: 185,363
Posted By netasha
Hi Brian, Do you think it is possible for...

Hi Brian,

Do you think it is possible for bbduk2.sh to trim both 5' end and 3' end with each mapping to a 22 nt reference and and a 3 nt reference, respectively?
To be more specific, the 5' end...
Showing results 1 to 8 of 8

 


All times are GMT -8. The time now is 04:20 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO