How do I determine if an mRNA was made with strand or non strand method?
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2.3 years ago
jaqx008 ▴ 110

HI, I am trying to figure out if my transcriptomic data (downloaded from ncbi) was made using strand or non strand method. This information was not provided alongside the download page. Is there a way I can do this using the fastq file? Thanks

RNA-Seq illumina Strand vs non strand • 486 views
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You can align it as a stranded library and look at the alignments on a genome browser. If the library was actually unstranded, you will see a roughly 50/50 split between the strands in the alignments at any given location/gene, but if the library was stranded then you will see a strong bias towards the strand that the gene is on.

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2.3 years ago
GenoMax 111k

Use infer_experiment.py from RSeQC after you align the data : RSeQC Output from infer_experiment.py - what does it mean?

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2.3 years ago
ATpoint 57k

You could quantify your data against a reference transcriptome with salmon and use the library type to automatic detection -l A. It will tell you then the most likely library type. Did you check the publication (if there is one) towards the method section / kit they used?

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Thank you for your suggestion. the paper wasnt on ncbi. however, i was able to search key words and found the paper. I have see that the reads were non-strand. Thank you