Question: counting reads with featureCounts - uniquely assign reads to transcripts
gravatar for Pfs
5.1 years ago by
United States
Pfs510 wrote:


I have a question regarding featureCounts behavior.

Assume my GTF file has 1 gene, comprising 2 transcripts (G1T1, G1T2), with a total of 3 exons (E1,E2,E3): 
G1T1 consists of exons E1 and E2, while G1T2 consists of exons E3 and E2. 

Assume my SAM file has 4 reads, as shown below.
R1 overlaps E1;
R2 is spliced between E1 and E3;
R3 is spliced between E1 and E2;
R4 is spliced between E3 and E2.

|____E1____|                   |____E2____|   Transcript G1T1
               |____E3____|    |____E2____|   transcript G1T2


When using featureCounts with option "-g transcript_id", only R1 is assigned and the counts for G1T1 is 1.
When using featureCoutns with option "-g transcript_id -O", all reads are assigned and the counts for G1T1 is 4 (R1,R2,R3,R4), whereas the count for G1T2 is 3 (R2,R3,R4).

I understand the logic behind allowing multiply overlapping features ("-O"), however I would expect that at the transcript level R3 is uniquely assigned to G1T1 and R4 uniquely assigned to G1T2. In other words, I would expect that even though the parts of a spliced read are mapped to multiple features, when the reads are counted at a level where a distinction between metafeatures is possible, this distinction is used to uniquely assign the reads.

I feel that without "-O", the counts are unnecessarily low and with the option "-O" the counts are unnecessarily inflated. What am I missing here?


Thanks in advance!

rna-seq counting reads • 3.7k views
ADD COMMENTlink modified 5.1 years ago by Devon Ryan96k • written 5.1 years ago by Pfs510
gravatar for Devon Ryan
5.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

One should really not use featureCounts (even with -O) to get transcript-level metrics. If you really want these numbers, use something like eXpress or another tool that has an expectation-maximization step.

BTW, what you're missing is that exon E2 is shared between both transcripts, so any alignment to it will necessarily by non-unique (aka ambiguous).

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Devon Ryan96k
gravatar for mark.ziemann
5.1 years ago by
mark.ziemann1.2k wrote:

Indeed, the counts can be quite low from featureCounts, but if you use the default gene-wise counting with stranded seq it is a bit better. The transcript-wise counting will be very strict without -O, especially for genes with many splice types, so you might have better luck with counting based on exons first followed by DEXSeq differential analysis. In featureCounts, you can use the -R option to see the read assignment result for each read to help you fine-tune further.

ADD COMMENTlink modified 9 months ago by RamRS28k • written 5.1 years ago by mark.ziemann1.2k
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