By default, STAR outFilterMultimapNmax parameter (read alignments will be output only if the read maps fewer than this value) is set to 10. Should that just be set to 1 if you are going to process the data with htseq-count, which discards multi-mapped reads? Is there a benefit to leaving it at 10?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by id0 View PostBy default, STAR outFilterMultimapNmax parameter (read alignments will be output only if the read maps fewer than this value) is set to 10. Should that just be set to 1 if you are going to process the data with htseq-count, which discards multi-mapped reads? Is there a benefit to leaving it at 10?
Whether multimappers are useful depends on your downstream analysis. I find it useful to generate wiggle tracks separately for unique and multi-mappers, sometimes you can miss expression if you only look at unique mappers. Also, other quantification software (e.g. Cufflinks) can "rescue" multi-mappers. Typically multimappers do not occupy a lot of space, and - if needed - can be easily filtered by NH flag or the MAPQ field.
Latest Articles
Collapse
-
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 -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment