Originally posted by jsun529
View Post
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Thank you very much for all your help, since I am very new to this BFAST program, The program runs pretty fast and with the new version it runs pretty smoothly. For my test run on solid, when I use the sam tools to call variants, the result was not what I expected, I think it comes to both side, one is the samtools, another is I think more critical as how to create proper indexes, for snp and indels? Looks like with new version this is the only parameter left to the user? Thanks
Comment
-
Originally posted by jsun529 View PostThank you very much for all your help, since I am very new to this BFAST program, The program runs pretty fast and with the new version it runs pretty smoothly. For my test run on solid, when I use the sam tools to call variants, the result was not what I expected, I think it comes to both side, one is the samtools, another is I think more critical as how to create proper indexes, for snp and indels? Looks like with new version this is the only parameter left to the user? Thanks
Comment
-
Hi Nils,
I found Bfast challenging to get into as well. I saw that as someone who has been using Maq, Mosaik, Bowtie and so on for quite some time now.
There is plenty of detail in the manual but the program expects you to set parameters right from the off, without any suggestion of defaults. Now it may well be this is complicated and reference dependent, but to encourage users I would strongly recommend
a) a short sample reference, say a genomic island or 500k of a genome
b) a few reads which can be mapped onto this.
There is plenty of public data about now.
Then I would have a group of command lines in place of the "quick tutorial" links.
For users unfamiliar with installing from c source instructions could be provided as well.
I m sure potential users would appreciate the effort involved in doing this
Colin
Comment
-
Originally posted by colindaven View PostHi Nils,
I found Bfast challenging to get into as well. I saw that as someone who has been using Maq, Mosaik, Bowtie and so on for quite some time now.
There is plenty of detail in the manual but the program expects you to set parameters right from the off, without any suggestion of defaults. Now it may well be this is complicated and reference dependent, but to encourage users I would strongly recommend
a) a short sample reference, say a genomic island or 500k of a genome
b) a few reads which can be mapped onto this.
There is plenty of public data about now.
Then I would have a group of command lines in place of the "quick tutorial" links.
For users unfamiliar with installing from c source instructions could be provided as well.
I m sure potential users would appreciate the effort involved in doing this
Colin
There is a quick tutorial at the end of the manual giving examples and the recommended parameters (the program now has defaults). Does this address the issue?
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-25-2024, 11:49 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
04-25-2024, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
62 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment