@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 ?
Illumina hiseq 2500 strand specificity for paired-end datasets
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?
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nnry06 •
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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.
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WouterDeCoster
Then look at the page linked by ahaswer : How to know that your RNA-seq is stranded or not?
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If you are not sure about the strandness of your data you can check it with Salmon as @Wayne has suggested in this post.