Hi All
I am a rookie in RNA-seq, and I have some problems.
I have tried the pipeline of Tuxedo (Tophat-Cufflinks-Cuffdiff) to analysis the data.
Now I want to change some other pipelines (DESeq or edgeR, etc) to compare the performance.
However, as you know, these R-based package need the software htseq-count to generate the annotated count matrix.
So I use this command but get the error:
htseq-count -m intersection-strict -s no accepted_hits.sam merged.gtf>subset.counts
where accepted_hits.sam is file convert from accepted_hits.bam which is generated by Tophat. merged.gtf is the merged annotation generated by Cufflinks-Cuffmerge.
Is something wrong I did?
Or I need to use the reference genome:
genes.gtf but not merged.gtf
which is GTF/GFF file I need to use? reference genome or assembled transcripts? Thank you!
I am a rookie in RNA-seq, and I have some problems.
I have tried the pipeline of Tuxedo (Tophat-Cufflinks-Cuffdiff) to analysis the data.
Now I want to change some other pipelines (DESeq or edgeR, etc) to compare the performance.
However, as you know, these R-based package need the software htseq-count to generate the annotated count matrix.
So I use this command but get the error:
htseq-count -m intersection-strict -s no accepted_hits.sam merged.gtf>subset.counts
where accepted_hits.sam is file convert from accepted_hits.bam which is generated by Tophat. merged.gtf is the merged annotation generated by Cufflinks-Cuffmerge.
Is something wrong I did?
Or I need to use the reference genome:
genes.gtf but not merged.gtf
which is GTF/GFF file I need to use? reference genome or assembled transcripts? Thank you!
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