Hi all, I generated sorted bam files for my samples using samtools after genome alignment by hisat2. Then I need to get read counts for differential expression analysis. Since I am working on a non-model organism, there is no genome annotation available (the genome gff file) so I assume that I could not use htseq since it requires the gff file. Then I considered using samtools idxstats but I noticed that it also includes unmapped and multi-mapped reads (is it?). So here is my question, is there a way I can get the proper count values using either of these two? Or I need to write my own codes for this purpose?
Suggestions are appreciated.
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For genome with a GTF or GFF file, use htseq-count (actually, featureCounts, which is faster). For an assembled transcriptome you'd be best off with salmon.
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Do you have any gene coordinates? Or is there an assembled transcriptome available? Please add details on what is available from that organism.
I obtained the genome from a senior in my lab. It's a scaffold genome with positional ID, I guess I could annotate the differentially expressed genes at last.
What does that mean? So you don't know where the genes actually are in the scaffolds or you do?
You need gene positions to do DEG in the first place. Positional ID, does that mean you know where the genes are?
You need gene positions to do DEG in the first place. Positional ID, does that mean you know where the genes are?
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