read count for RNA sequencing via nanopore
Hi all,
I have some long reads sequencing data of Oxford nanopore technology. I mapped reads to the human genome via minimap2, mapping makes sense but as expected, there are many seq errors and gap openings. Now I want to have read count per gene. For this end I tried to run Salmon, using an indexed human transcriptome, but most of the reads were filtered out due to low alignment score.
What is the best practice for RNA-seq quantification of long read data?
thanks a lot! Gat.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Bambu on illumina short reads sequencing
written by Simone •
-
Removing duplicates
written by quentinperriere •
-
Does salmon work with combined short and long read bam file?
written by shinyjj •
-
filter reads with >90% match
written by anuradharavi10 •
-
salmon with long reads
written by shinyjj •
-
Whole transcriptome
written by a.fathi •
-
Question regarding minimap2 presets
written by Rogerio Ribeiro •
-
What are best Long read simulator generating Oxford Nanopore Reads
written by Ashi •
-
Using DESeq2with Oxford Nanopore Technology Direct RNA Sequencing
written by uhlkatie •
-
trimming nano pore reads based on quality score.
written by KVC_bioinfo
Have you checked the pipeline provided by ONT?
GenoMax makes a good suggestion. Generally the next step would be use of a tool like FeatureCounts or htseq-count to get the read counts.
AFAIK Salmon is a kmer tool intended for short reads, so not applicable here.