How to know library types of public datasets ?

Question

[Angelique]

Good morning,

I want to analyse public SHort Read archive from an RNA-seq experiment. I am trying to quantify them using sailfish. it is needed to provide the library type as an argument : -l "<libtype>" But I only that my data are paired-end ( dataset GSE89063) How can I know what to write for this argument ? Thanks a lot

Have a good day

[ATpoint]

Is there a reason you use Sailfish and not Salmon, which is more recent, and has an option to detect the library type?

[Angelique]

I already tried salmon, I wanted to compare the results between Salmon and Sailfish

Answer 1

[ferozef]

Hi, You can also check by performing some steps to know the strand specificity, please check the link below.

http://onetipperday.sterding.com/2012/07/how-to-tell-which-library-type-to-use.html

Hope it works with you.

Answer 2

[pbpanigrahi]

Excellent resource to read

Unstranded

Kits:

TruSeq RNA Sample Prep kit

Parameters:

• HISAT2 / TopHat / Cufflinks / Cuffdiff: library-type fr-unstranded
• HTSeq: stranded -- no

Directional, first strand:

Kits

• All dUTP methods, NSR, NNSR
• TruSeq Stranded Total RNA Sample
• Prep Kit TruSeq Stranded mRNA Sample Prep Kit
• NEB Ultra Directional
• RNA Library Prep Kit Agilent SureSelect Strand-Specific

Parameters:

• HISAT2 / TopHat / Cufflinks / Cuffdiff: library-type fr-firststrand
• HTSeq: stranded -- reverse

Directional, second strand:

Kits:

• Directional Illumina (Ligation), Standard SOLiD
• ScriptSeq v2 RNA-Seq Library Preparation Kit
• SMARTer Stranded Total RNA
• Encore Complete RNA-Seq Library Systems
• NuGEN SoLo

Parameters:

• HISAT2 / TopHat / Cufflinks / Cuffdiff: library-type fr-secondstrand
• HTSeq: stranded -- yes

So first go to SRA and check which protocol they have used, whether strand specific or not. If strand specific, then which strand, that you can know by the kit they use.

Hope this helps

[Angelique]

Thanls a lot I am goind to take a look at this ressource

Answer 3

[apaytuvi]

For that, we follow the approach AIR (https://transcriptomics.sequentiabiotech.com) uses. You should need a BAM file and an annotation file (BED file with the exon coordinates and the corresponding strand). Afterwards, you can use:

http://rseqc.sourceforge.net/#infer-experiment-py

To know whether the data is stranded or unstranded.

[Ram]

Please do not use the forum to advertise your product, especially one that is not FOSS.