Hi everyone,
I'm doing mouse transcriptome analysis using Tophat-Cufflinks work flow, and I met a confused problem.
I have 8 samples, each of them has a replicate, so I have 16 samples of RNA-seq data. Then I remove adaptors using cutadapt. Tophat was performed with fastq data without adaptors, so I got a mapping rate around 80%. Tophat runs with default parameters. Then I use cufflinks on accepted_hits.bam files from Tophat (default parameters).
14 samples went well on this but 2. Let's name them A and A-rep.
21570 genes expressed in sample A, while only 364 genes expressed in A-rep. (FPKM value > 0 means gene expressed)
So I searched for the error file, and it gives me a warning
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.
What's the meaning of this message? Because it went well on my other samples...
Many thanks!
I'm doing mouse transcriptome analysis using Tophat-Cufflinks work flow, and I met a confused problem.
I have 8 samples, each of them has a replicate, so I have 16 samples of RNA-seq data. Then I remove adaptors using cutadapt. Tophat was performed with fastq data without adaptors, so I got a mapping rate around 80%. Tophat runs with default parameters. Then I use cufflinks on accepted_hits.bam files from Tophat (default parameters).
14 samples went well on this but 2. Let's name them A and A-rep.
21570 genes expressed in sample A, while only 364 genes expressed in A-rep. (FPKM value > 0 means gene expressed)
So I searched for the error file, and it gives me a warning
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.
What's the meaning of this message? Because it went well on my other samples...
Many thanks!
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