Question: Illumina hiseq 2500 strand specificity for paired-end datasets
0
gravatar for nnry06
4 months ago by
nnry060
nnry060 wrote:

For the RNA-Seq analysis, i am using paired-end datasets that has been generated from Illumina HiSeq 2500 (Homo sapiens). I have used the following command for quantification,

featureCounts -F GTF -t exon -g gene_id -O -s 0 -a 'GRCh38.96.chr.gtf' -o count_from_ensembl.txt SRRXXX*.bam

In output, both '+' and '-' strand are there in the strand column. I am not able to understand whether its correct or not. Is illumina Hiseq 2500 is strand specific? if not, then how to know whether the reads are stranded or unstranded?

ADD COMMENTlink modified 4 months ago by WouterDeCoster42k • written 4 months ago by nnry060

If you are not sure about the strandness of your data you can check it with Salmon as @Wayne has suggested in this post.

ADD REPLYlink modified 4 months ago • written 4 months ago by ahaswer150
1
gravatar for WouterDeCoster
4 months ago by
Belgium
WouterDeCoster42k wrote:

Is illumina Hiseq 2500 is strand specific?

Strand-specificity does not depend on the sequencer used for your samples, but for the library preparation kit.

ADD COMMENTlink written 4 months ago by WouterDeCoster42k

@WouterDeCoster, The name of the library preparation kit used has not been mentioned in the paper from where i took the datasets. So, i am not being able to understand whether the reads of the datasets are stranded or unstranded. Can you please guide me in this ?

ADD REPLYlink written 4 months ago by nnry060

Then look at the page linked by ahaswer : How to know that your RNA-seq is stranded or not?

ADD REPLYlink modified 4 months ago • written 4 months ago by WouterDeCoster42k
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