Question: Cutoff of reads in htseq
gravatar for olga.lubinsky
5.6 years ago by
European Union
olga.lubinsky0 wrote:


To my understanding the standard number of cutoff for falsely expressed genes in trancriptome is 30 reads.

Am i right? and what is the reason for a this specific cutoff?

Thank you


rna-seq • 1.8k views
ADD COMMENTlink modified 5.6 years ago by Martombo2.6k • written 5.6 years ago by olga.lubinsky0

Can you explain more ? As the heading of question, htseq, there is no min or max cutoff to calculate no. Of read/fragments mapped per genomic location. If you are talking about the differential expression, the cutoff will be based on statistical test but not on any standard number.

If you can provide any source for your understanding, that would be good.

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by geek_y11k
gravatar for Devon Ryan
5.6 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

There is no standard cut-off and there could never be one. The best practice is to use independent filtering.

ADD COMMENTlink written 5.6 years ago by Devon Ryan96k
gravatar for Martombo
5.6 years ago by
Seville, ES
Martombo2.6k wrote:
there is no standard threshold. you can use the one that is more suitable for your data. in deseq2 you will find an implementation of the independent filtering, suggested by Devon. it basically sets the threshold in a way to get the highest number of differentially expressed calls. check it afterwards, since it could be too high (or too low), depending on your expectations.
ADD COMMENTlink written 5.6 years ago by Martombo2.6k

I'm not dealing with differentialy expressed gene but with the transcriptome itself. 

I have the reads of each gene , how do i decide wich number of reads is too low to consider as a signficantly expressed gene?

ADD REPLYlink written 5.6 years ago by olga.lubinsky0

There's no standard for that as well (there never could be). The best you can do is plot the FPKM/RPKMs and see if you have an obviously bimodal distribution. If not, you're left with using the top X% as expressed.

ADD REPLYlink written 5.6 years ago by Devon Ryan96k

Hello Devon, can i ask you after the observing the bimodal distribution, which steps do you suggest for filtering, im dealing with tpm. Thanks in advance

ADD REPLYlink written 2.8 years ago by lessismore880
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