Question: RNAseq_Rsubread_transcript variants detection
0
gravatar for tarek.mohamed
3.6 years ago by
tarek.mohamed10 wrote:

Hi All,

 I am using it to analyze RNAseq data from different samples with and without treatment.

I am looking at a certain gene with 5 transcript variants  and I want to know which of splice variants are expressed in my samples.

I ran 

Is there a way by which I can know?

Thanks

 

 

rnaseq • 415 views
ADD COMMENTlink modified 3.6 years ago by etycksen0 • written 3.6 years ago by tarek.mohamed10

Can you provide more info about what you have done in your analysis? Given the limited info you provided it is hard for people to help you.
 

ADD REPLYlink written 3.6 years ago by Wei Shi3.2k
Answer: RNAseq_Rsubread_transcript variants detection
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gravatar for etycksen
3.6 years ago by
etycksen0
etycksen0 wrote:

The Subread featureCounts functions works great for enumerating unique or multi-mapped reads to genes, but is not the best tool for estimating counts for splice variants due to the added complexity of reads aligning across and between splice junctions for splice variants that contain the same exons.  Tools such as eXpress, Sailfish, Salmon, or RSEM that use an expectation-maximization algorithm to estimate counts for splice variants are probably your best bet, but those tools are outside the realm of both R and Bioconductor.  If you have transcriptome aligned bam files, eXpress and RSEM will work well for you.  If you have a genome aligned bam file, Salmon will serve you well.  Alternatively, Sailfish can operate on unaligned fastq files and you can generate custom indexes of known and putative splice variants (splice variants reported in literature that are not present in databases such as Ensembl) as long as you have the fasta sequence.  Good luck and I hope this helps.

ADD COMMENTlink written 3.6 years ago by etycksen0
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