I like the presentation (heatmap table). Could you try varying the "-K" and "-M" parameters? Alternatively, you could design indexes with greater key size (more ones in the mask). There is a lot of flexibility, though I haven't thought about longer read lengths. The only criticism I have is that short-read aligners are designed for short-reads, and you are using them in a non-standard way; just like BLAT would not be used for 35bp error-prone reads.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Yes actually the point of the study is to determine how they behave with different read lengths. Most mappers are made for say 50bp, but what about 55 or 45 or 60...? The problem is that my type of reads ( from 4C / Hi-C / 3C ) don't have nice single size reads. That's why I'm testing each aligner to see where it is the strongest and where it is the weakest. My hope is that I can combine 2 or more programs to have a complete solution.
My question for BFast is because I thought that a longer read would generate more CALS and therefore, all things being equal, would be easier to map ... which is what happens in Blat... anyway I will try to mess around with BFast a bit moreLast edited by aleferna; 08-01-2010, 10:47 AM.
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
Comment