Hi everyone,
When I run Cuffcompare on the merged.gtf I get from Cuffmerge, the FPKM values are zero in the tmap. Does anyone have any idea why this might happen? Running Cuffcompare on individual the individual tissues gives me FPKM values. I did not get an errors in when running anything except when I ran Cuffmerge I got:
[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).
File set_1_merge/tmp/mergeSam_fileHkhL9l doesn't appear to be a valid BAM file, trying SAM...
But Cuffmerge completed without any errors. I'm not really sure what file Cuffmerge is looking for. Any information on how Cuffmerge works is greatly appreciated.
Thank you.
When I run Cuffcompare on the merged.gtf I get from Cuffmerge, the FPKM values are zero in the tmap. Does anyone have any idea why this might happen? Running Cuffcompare on individual the individual tissues gives me FPKM values. I did not get an errors in when running anything except when I ran Cuffmerge I got:
[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).
File set_1_merge/tmp/mergeSam_fileHkhL9l doesn't appear to be a valid BAM file, trying SAM...
But Cuffmerge completed without any errors. I'm not really sure what file Cuffmerge is looking for. Any information on how Cuffmerge works is greatly appreciated.
Thank you.
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