Question: Sorting BAM files from HISAT2 for DEXSeq
gravatar for squando
2.1 years ago by
squando10 wrote:

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?


hisat2 rna-seq dexseq • 1.1k views
ADD COMMENTlink modified 2.1 years ago by Ian5.7k • written 2.1 years ago by squando10

HISAT2 output is probably unsorted, you can check with:

samtools view -h file.bam | grep 'SO:'
ADD REPLYlink written 2.1 years ago by h.mon31k

Instead than using Htseq-count try featureCounts it's much faster.

ADD REPLYlink written 2.1 years ago by Arup Ghosh2.7k
gravatar for Ian
2.1 years ago by
University of Manchester, UK
Ian5.7k wrote:

If in any doubt just rerun 'samtools sort'. Remember if you have multiple processors then use '-@ N', where N is the number of processor cores.

ADD COMMENTlink written 2.1 years ago by Ian5.7k
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