Question: Sorting BAM files from HISAT2 for DEXSeq
0
gravatar for squando
3 months ago by
squando10
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?

Thanks!

hisat2 rna-seq dexseq • 255 views
ADD COMMENTlink modified 3 months ago by Ian5.3k • written 3 months ago by squando10
2

HISAT2 output is probably unsorted, you can check with:

samtools view -h file.bam | grep 'SO:'
ADD REPLYlink written 3 months ago by h.mon23k

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

ADD REPLYlink written 3 months ago by arup820
0
gravatar for Ian
3 months ago by
Ian5.3k
University of Manchester, UK
Ian5.3k 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 3 months ago by Ian5.3k
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