This is a test version of Biostars. For the public version, visit https://www.biostars.org.
What is the best tool for estimate the counts of genes with very low expression rate ?

i looking for a tool which can give me "count number" for very low expression rate genes or pseudogenes like PER3. What is the best tool for estimate the counts of genes with very low expression rate ? or the best aligner or aligner options to get me maximum amount of fragments to recognize with a FeatureCount or some tools like that.

gene rna-seq alignment
• 1,362 views • link
updated by Ram Ram • written by sabaghianamir70 • sabaghianamir70

Can you give some details, especially why standard approaches like counting reads over a GTF file that contains these genes with e.g. featureCounts does not help here?

• 0 views • link
written by ATpoint ATpoint

There is nothing special about lowly-expressed genes when it comes to processing of the data. You can use any of the established tools be it hisat2 followed by featureCounts or salmon followed by tximport. I use the latter one as it takes proper care of multimappers and corrects for GC bias.

• 0 views • link
written by ATpoint ATpoint

if i want to get maximum amount of reads, which means map every read even the false one, So. first.:what option should i use(salmon options)? and second: i want filter the false reads with FDR and p value .(is it Right strategy?).i asking because i think you are working on this matter.

• 0 views • link
written by sabaghianamir70 • sabaghianamir70

I strongly recommend against tweaking alignment/mapping parameters that are well-established. I would use salmon to quantify your reads against the reference transcriptome and then take whatever quantification it produces. I do not see the benefit in accumulating false-positives.

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this