Question: Cufflinks: Why in the skipped gtf file showed a portion of genome masked
0
gravatar for mjoyraj
4.6 years ago by
mjoyraj50
Taiwan
mjoyraj50 wrote:

I mapped my RNA-se reads with Tophat with the commands

Tophat –p 8 –o output –I 20000 –g 5 –G gtf_file Genome Fastq1 fastq2

Then I assembled the aligned tophat bam file using cufflinks with the commands

Cufflinks –p 20 –o output accepted.bam file

I found some of the genes are not assembled and they are masked as can be seen in skipped.grf.

I wonder why this has happened…?? Can anybody suggest something

 

rna-seq cufflinks assembly • 2.0k views
ADD COMMENTlink modified 4.6 years ago by Devon Ryan91k • written 4.6 years ago by mjoyraj50
2
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:
  1. That tophat command is appropriate for PE mapping. You need to separate the fastq files with commas (no spaces!).
  2. If coverage is too high then cufflinks will skip a region.
ADD COMMENTlink written 4.6 years ago by Devon Ryan91k

Yes, I observed the skipped region are mostly my target genes which are highly expressed (as can be seen from mapped reads). So I am trying again cufflinks-assembly with "--max-bundle-frags 1000000000000".

ADD REPLYlink written 4.6 years ago by mjoyraj50
1

Something like that, I always have to look up cufflinks parameters.

ADD REPLYlink written 4.6 years ago by Devon Ryan91k

Thanks.... Ryan

ADD REPLYlink written 4.6 years ago by mjoyraj50

Dear Ryan, when I used "--max-bundle-frags 1000000000000" in cufflinks, the run continues for a long time and it is still running showing waiting for two threads to complete. Is it okay?. Do I need to increase the number of threads??

ADD REPLYlink written 4.6 years ago by mjoyraj50
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