You can use RSeQC's read_distribution.py function (with a given bed file) to get a first glance at your data.
With HTSeq-count you get the gene read count. (Be aware of the strand information of your data). Additionally, if your gtf has information of the genes' bio-type (protein_coding, rRNA, etc.), you can count the reads for each of these classes.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
BEDTools multicov: http://bedtools.readthedocs.org/en/l.../multicov.html
If you need a visual program: http://seqanswers.com/forums/showthread.php?t=47028
Samtools depth option: http://seqanswers.com/forums/showthread.php?t=45399
Leave a comment:
-
number of reads per region of interest
Hello,
I want to calculate the number of reads mapped to my reference in each gene, in the intergenic regions, in introns, in rRNA and tRNA.
I have bam and gff files. Which commands can I use?
Thanks for your helpTags: 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, 07-25-2024, 06:46 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
07-25-2024, 06:46 AM
|
||
Started by seqadmin, 07-24-2024, 11:09 AM
|
0 responses
26 views
0 likes
|
Last Post
by seqadmin
07-24-2024, 11:09 AM
|
||
Started by seqadmin, 07-19-2024, 07:20 AM
|
0 responses
160 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: