Questions tagged [strandedness]

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HISAT2: RNA strandedness

My library is unstranded and the code I'm trying to use is this: ...
3 votes
1 answer

Discrepancy with featurecounts analysis using a forward stranded and reverse stranded protocol

My RNAseq analysis pipeline is as follows: fastqc (read quality is good, some overrepresentation of adaptor sequence) → trimmomatic (trimmed adaptor sequence, qc report after trimming suggests the ...
2 votes
1 answer

Why is there antisense sequence in RNAseq data

I'm looking at RNAseq data from CCLE. The data is paired-end. Take the cell line Hs578T and the gene HRAS as an example. The cell line carries a G12D mutation (c.35G>A), so the change in cds is: <...
4 votes
0 answers

R package equivalent to RSeQC infer_experiment to get strandedness of RNA-Seq

I am currently writing an R package that includes a module to run featureCounts (gene quantification tool) from Rsubread. I wanted to be able to specify the correct strandedness option to ...
9 votes
0 answers

Run cuffcompare in strand-agnostic mode

Is there a way to run Cufflinks' cuffcompare in a strand-agnostic mode? I would like to do this because I have some RNA-seq datasets derived from an unstranded run, that should be compared to a ...
1 vote
1 answer

How to detect bedtools version used by pybedtools (in order to correctly preserve strand information when merging gtf records)

I have issues working with pybedtools due to strand information being lost after extracting and merging transcript coordinates from a gtf file. It seems that the solution to preserve strand ...
0 votes
2 answers

Does rRNA depletion protocol give higher number of mapped reads in Intronic regions?

Recently, I have downloaded a publicly available dataset, which are 350 tumor samples. I see the following information from the published paper. They used Ribo Zero Gold and rRNA was depleted. Strand ...
1 vote
4 answers

At what processing step should library strandedness type be taken into account?

Suppose I have single-end RNA-seq data for which the reads in the fastq file are reversed with respect to the original extracted RNAs. Suppose I have the following workflow: Map the reads on the ...