Question: Detecting a small set of given Intron-Exon junctions in a RNA-Seq dataset
1
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

Hi all, I've been given a set of RNA-Seq fastqs (4 samples) and a collaborator would like to know how many defined intron-exon junction in his favorite gene are detected in those reads.

My idea was to clean the reads with cutadapt, align with Bowtie and create a custom program to loop over the cigar string and detecting the junctions.

or is there an existing tool for this ? Bonus if the tool can tell me wether two junctions belong to the same transcript.

junction rna-seq intron exon • 1.6k views
ADD COMMENTlink modified 4.1 years ago by Malachi Griffith18k • written 4.1 years ago by Pierre Lindenbaum128k
2
gravatar for igor
4.1 years ago by
igor10k
United States
igor10k wrote:

If you use the STAR aligner, it will output SJ.out.tab with high confidence collapsed splice junctions in tab-delimited format.

ADD COMMENTlink written 4.1 years ago by igor10k

that was simple and it workded fine, thanks

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum128k
3
gravatar for Malachi Griffith
4.1 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

You can use the tool RegTools to get this information from a BAM file. So you would align your reads to the reference genome first using TopHat2, STAR, HISAT2, etc. Then use regtools to both extract and annotate the exon-exon junctions (i.e. exon-intron ... intron-exon). The

Code is here: https://github.com/griffithlab/regtools

Documentation is here: https://regtools.readthedocs.io/en/latest/

You would start with regtools junctions extract followed by regtools junctions annotate

Usage looks like this:

regtools junctions extract [options] indexed_alignments.bam
regtools junctions annotate [options] junctions.bed ref.fa annotations.gtf

The annotate result will among other things, tell you which junctions correspond to which transcripts, what novel junctions might be observed in your RNA-seq data, how these relate to known transcripts, etc. The annotations.gtf file could be a list of known transcript annotations. For example, we often use the GTF files that you can down directly from Ensembl.

ADD COMMENTlink written 4.1 years ago by Malachi Griffith18k
2
gravatar for Khader Shameer
4.1 years ago by
Manhattan, NY
Khader Shameer18k wrote:

I have used MapSplice, better to use their recent version MapSplice 2

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

ADD COMMENTlink written 4.1 years ago by Khader Shameer18k
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