Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Bowtie can do color-space, Bowtie2 cannot (and is not likely to in the future).
Leave a comment:
-
No, I haven't [yet] bothered with looking at another program. While I might get a higher proportion of mapped reads, I've got enough problems working with error in the reads I have from Bowtie.
Leave a comment:
-
1) What exactly is the difference between the F3 and F5 reads? Is the F5 reversed?
I think the 5' read is reverse and done first, so if you're doing an analysis taking reads in the usual order you need to specify RF orientation in the mapping program (I'm not very sure on this point).
3) Does the csfasta conversion work differently with paired-end data?
Leave a comment:
-
Understanding paired-end SOLiD
Hello everyone,
I am working with paired-end SOLiD data, and I am not sure how to handle it.
1) What exactly is the difference between the F3 and F5 reads? Is the F5 reversed?
2) I'm using BWA for the analysis. How do I use it with paired-end? In the documentation it says 'file 1' and 'file 2', but I don't know which is which.
I have tried to run it both ways and in both times I got very few variants - 3000, 5000 while expecting 50000.
I have a color-space reference index, and I used the -c parameter in the alignment. Am I missing something?
3) Does the csfasta conversion work differently with paired-end data?
Thanks a lot,
Amit
=]Tags: None
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
18 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
|
Leave a comment: