Getting warning while using cuffnorm - "Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided." #112
**Hi,
During cuffnorm for 18 samples run getting this warning (9 times and ):
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided.
I tried to investigate that myself and I got these:
Cufflink assembly stdout:**
**[14:43:30] Loading reference annotation.
[14:43:30] Inspecting reads and determining fragment length distribution.
**So here, fragment length mean and std-dev is calculated based on SAM alignment.
But while merging:**
[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 assembled_unique/tmp/mergeSam_file8AmUL8 doesn't appear to be a valid BAM file, trying SAM...
[04:06:36] Loading reference annotation.
[04:06:36] Inspecting reads and determining fragment length distribution.
Processed 1884 loci.
**So cuffmerge is applying default fragment length related parameter while merging, Thus cuffnorm is showing the warning I am getting.
I tried to define --frag-len-mean and --frag-len-std-dev to the any of these two steps, but didn't find any options. So, my question is whether it will cause any problem to the assembly and abundance calculation.**
**Hi, During cuffnorm for 18 samples run getting this warning (9 times and ):
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided.
I tried to investigate that myself and I got these:
Cufflink assembly stdout:**
**[14:43:30] Loading reference annotation. [14:43:30] Inspecting reads and determining fragment length distribution.
**So here, fragment length mean and std-dev is calculated based on SAM alignment.
But while merging:**
[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 assembled_unique/tmp/mergeSam_file8AmUL8 doesn't appear to be a valid BAM file, trying SAM... [04:06:36] Loading reference annotation. [04:06:36] Inspecting reads and determining fragment length distribution. Processed 1884 loci.
**So cuffmerge is applying default fragment length related parameter while merging, Thus cuffnorm is showing the warning I am getting.
I tried to define --frag-len-mean and --frag-len-std-dev to the any of these two steps, but didn't find any options. So, my question is whether it will cause any problem to the assembly and abundance calculation.**
Thanks!