that was simple and it workded fine, thanks
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Pierre Lindenbaum
Detecting a small set of given Intron-Exon junctions in a RNA-Seq dataset
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.
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Malachi Griffith
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Pierre Lindenbaum
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Pierre Lindenbaum
3 answers
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.
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Malachi Griffith
I have used MapSplice, better to use their recent version MapSplice 2
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
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Khader Shameer
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