Error running cuffdiff using SAM generated from GSNAP/GMAP
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5.7 years ago
kandoigaurav ▴ 150

I generated SAM files using GSNAP. Sorted them using the following command:

 

sort -k 3,3 -k 4,4n identifier.unpaired_uniq > file

 

Now, I'm able to run cufflinks but when I run cuffdiff, it says:

 

([bam_header_read] EOF marker is absent. The input is probably truncated.

[bam_header_read] invalid BAM binary header (this is not a BAM file).

[17:10:05] Loading reference annotation.

[17:10:08] Inspecting maps and determining fragment length distributions.)

 

And then keeps running. It's been days but it is still running. Here is the cuffdiff command:

 

cuffdiff merged_asm/merged.gtf P1_02.uniq.sorted,P2_02.uniq.sorted Control_P1_12.uniq.sorted,Control_P2_12.uniq.sorted,Control_P1_13.uniq.sorted,Control_P2_13.uniq.sorted -o diff_out.P_02vsContol -p 8 -L P,Control

 

Can someone point out where I'm going wrong?

Thanks

RNA-Seq GSNAP GMAP Cuffdiff Cufflink • 1.6k views
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Seems that the header info in the sorted file is at the bottom!

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Never use the unix sort command on SAM files, use samtools or picard. Secondly, do yourself a favor and sort the BAM files instead, they can then be indexed, which will likely make cuffdiff happier.

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