You could also enforce behavior #2 by first collapsing your read alignments to the set with the lowest edit distance (NM tag if you use BAM).
Aaron
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
The read is counted for both gene A and gene B. You could enforce behavior #3 if you first intersected the reads against your gene file and threw away all reads having a count (-c option) > 1.
For more complicated rules, I suggest the HTSeq package.
Aaron
Leave a comment:
-
BEDTools..coverageBed query
Hi
I have a question regarding the way BEDtools' coverageBed handles a short read that matches both gene A and Gene B. In such an instance could you let me know which of the following is true?
1. The read is counted for both Gene A and Gene B.
2. The read is counted for the gene which shows lower number of mismatches.
3. The read is thrown out.
thanks
SivaTags: None
Latest Articles
Collapse
-
by seqadmin
The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
Channel: Articles
07-08-2024, 03:19 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
159 views
0 likes
|
Last Post
by seqadmin
07-19-2024, 07:20 AM
|
||
Started by seqadmin, 07-16-2024, 05:49 AM
|
0 responses
127 views
0 likes
|
Last Post
by seqadmin
07-16-2024, 05:49 AM
|
Leave a comment: