Hi everyone, I'm new to RNA seq and still have trouble with all the nuances of bioinformatics as I do my analysis. I used HISAT2 to map all my reads to my reference genome (mouse), and have used htseq-count to continue with my differential gene expression analysis and statistics.
However, I'm also interested in looking at my reads on the exon level, and many forum posts here have suggested DEXseq. One of the run settings asks for the "Sorting order of alignments", but I can't figure out how the BAM file alignment output from HISAT2 is sorted. Should I just sort all of my BAM files using SAMtools, or does anyone happen to know how I can find out how my alignments are sorted?
Thanks!
1 answer
Log in to answer this question.
-
RNA-seq analysis
written by sk_24 •
-
filterBam (Augustus) results explanation
written by Sanam •
-
Proper HTSeq usage on bacterial genome. Don't quite understand --t
written by SushiRoll •
-
BWA mem bam output name sorted
written by User000
-
Difficulty mapping Ribo-seq reads to annotated transcriptome features
written by jpcchoy •
-
coordinate-sorted versus name-sorted bam file
written by bnayer26 •
-
Help interpreting error from DEXSeq
written by squando •
-
Question: Error HISAT2 output for HTseq-count
written by 11yj3312 •
-
HTSeq-count no feature is too high
written by sandeepmarla •
-
htseq-count for RNA Seq
written by Ron
HISAT2 output is probably unsorted, you can check with:
Instead than using Htseq-count try featureCounts it's much faster.