Aligned to mm10 using bowtie2, and converted to a sorted bam using samtools. How do I analyze my reads and what transcripts they correspond to
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by westerman View PostI'd drop the bowtie2 and instead use Tophat2 (which granted, will use bowtie2 internally but will also do better analysis).
Comment
-
Originally posted by KnowNothing2 View PostI had a question about that. Does bowtie2 throw reads out if they overlap at a splice junction since you're referencing to a genome ?
I point out that Tophat2 does not use '--local' but rather '--end-to-end'. It can do this because it actually splits up reads into smaller segments that should map end-to-end and not need the soft-clipping that 'local' generates.
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, Yesterday, 07:03 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 07:03 AM
|
||
Started by seqadmin, 05-10-2024, 06:35 AM
|
0 responses
35 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
41 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
36 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
Comment