Question: RNAseq RSEM and featurecounts
0
gravatar for sidwell
15 days ago by
sidwell10
sidwell10 wrote:

I use RSEM to count abundance of each transcript after alignment with STAR and featureCounts to count abundance of each transcript after alignment with Bowtie.

My question is, if a read map on a given location of the genome, but at this location, there are multiple transcripts overlapping : How RSEM or featureCounts decide which transcript is it ?

For example, in the mouse at this location : https://www.ensembl.org/Mus_musculus/Location/View?r=7:44804176-44853021;db=core;g=ENSMUSG00000074141
You can see il4i1 and nup62 are overlapping.

But in my counts table, I have a big difference between abundances of those 2 genes. Why ?

rna-seq alignment • 115 views
ADD COMMENTlink modified 15 days ago by igor11k • written 15 days ago by sidwell10
2
gravatar for h.mon
15 days ago by
h.mon31k
Brazil
h.mon31k wrote:

Mapping to the transcriptome will result in a high rate of reads mapping to multiple locations, due to the multiple isoforms present in a transcriptome. RSEM will use an expectation-maximization to optimally assign (fractional) counts from multi-mapping reads, while featureCounts will, with default settings, discard all multi-mapping reads.

ADD COMMENTlink written 15 days ago by h.mon31k

I thought multi-mapping reads was about a read which is mapping at multiple locations. But here my read map at ONE position. But this position is corresponding to multiple transcripts.

ADD REPLYlink written 15 days ago by sidwell10
1

The same applies to reads assigned to overlapping features: featureCounts discards them, RSEM tries to optimally assign the counts.

ADD REPLYlink written 15 days ago by h.mon31k
1
gravatar for swbarnes2
15 days ago by
swbarnes29.2k
United States
swbarnes29.2k wrote:

I think that because Featurecounts is not smart about reads whose assignment is ambiguous, it is not suitable for assessing transcript abundance. Genes would be okay, exons would be okay, but not transcripts.

ADD COMMENTlink written 15 days ago by swbarnes29.2k
1
gravatar for igor
15 days ago by
igor11k
United States
igor11k wrote:

For overlapping genes, featureCounts is similar to HTSeq-count, which has a nice graph showing you the various options:

enter image description here

ADD COMMENTlink written 15 days ago by igor11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1304 users visited in the last hour