Error in htseq count "Please provide two arguments"

[super0925]

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!

[super0925]

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
Thank you!

which is GTF/GFF file I need to use? reference genome or assembled transcripts? Thank you!

[Simon Anders]

Are you sue the command you typed is exactly as you posted it here? The error message means that you did not specify two files -- it is generated before the script actually looks into the files, so it has nothing to do with their content.

[super0925]

Are you sue the command you typed is exactly as you posted it here? The error message means that you did not specify two files -- it is generated before the script actually looks into the files, so it has nothing to do with their content.

I am sure.
But when I tried the genes.gtf, it works. but merged.gtf, it is not working.