Questions tagged [strandedness]
The strandedness tag has no usage guidance.
9 questions
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I have assembled raw short RNA-seq reads into Transcripts using Trinity. My raw reads were strand-specific. What should I set "--strand" in Diamond?
I used Trinity to de-novo assemble my RNA seq raw reads. These reads were generated using a strand-specific method. Now I want to do a BLASTx using Diamond. I am unsure what I should keep under its ...
- 69
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HISAT2: RNA strandedness
My library is unstranded and the code I'm trying to use is this:
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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 ...
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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:
<...
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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 ...
- 3,205
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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 ...
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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 ...
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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 ...
- 2,716
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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 ...
- 3,205