I am going to perform transcriptome analysis.Which is better tool for transcriptome analysis Usegalaxy Server or DNA Star? Kindly suggest me. Thanks in advance.
Thank you much ATpoit and kristoffer.vittingseerup for too quick reply
I have four paired end raw data seq files of two sample. Sample-1 has two file (forward and reverse) and sample-2 has two files (forward and reverse).
The uncompressed size of each file is approx GB. I want to construct de novo transcriptome using these raw data files. After de novo transcriptome construction I want to differential expression, isoform detection, mutations and SNP identification both samples. These SNP will be used for genotyping.
For this purpose I started working with usegalaxy server. Firstly, I concatenated the forward and reverse files into single files of both samples at web based usegalaxy sever. These concatenated files Fastqc assessment. Some attribute in Fastqc report are failed but most of the passed.
At this stage someone has suggested me that you going in wrong direction and he advised me to first check the read alignment of forward raw sequences and reverse raw sequence. He said if these reads show 100% alignment then used single raw data file (Forward or Reverse) from each samples. He also advised me to work with DNA Star instead of usegalaxy server.
Kindly guide me the right direction with some user friendly tools and principle.
Sounds like you are going to need help no matter which program you use.
If you have a license for DNASTAR transcriptomics module then you can call on their tech support to provide assistance as needed. You could do the same with Galaxy but then you will be relying on community support that may not be as prompt or complete as you expect/need.
Since you're interested in using Galaxy for this, please go through this example workflow for a nice example of de novo transcriptome assembly in Galaxy.
Note that with only 2 samples you cannot perform differential expression reliably with any tool in any platform.
Thank you so much Devon Rayon !
Is there a another way to perform the differential DGE analysis. Can I take SRA sequences ( Available at NCBI) and use as control. Is it possible? Kindly guide me.
What is the question, differential expression, isoform detection, mutations...?
Could you elaborate on what your question is?
Thank you much ATpoit and kristoffer.vittingseerup for too quick reply
I have four paired end raw data seq files of two sample. Sample-1 has two file (forward and reverse) and sample-2 has two files (forward and reverse).
The uncompressed size of each file is approx GB. I want to construct de novo transcriptome using these raw data files. After de novo transcriptome construction I want to differential expression, isoform detection, mutations and SNP identification both samples. These SNP will be used for genotyping.
For this purpose I started working with usegalaxy server. Firstly, I concatenated the forward and reverse files into single files of both samples at web based usegalaxy sever. These concatenated files Fastqc assessment. Some attribute in Fastqc report are failed but most of the passed.
At this stage someone has suggested me that you going in wrong direction and he advised me to first check the read alignment of forward raw sequences and reverse raw sequence. He said if these reads show 100% alignment then used single raw data file (Forward or Reverse) from each samples. He also advised me to work with DNA Star instead of usegalaxy server.
Kindly guide me the right direction with some user friendly tools and principle.
Sounds like you are going to need help no matter which program you use.
If you have a license for DNASTAR transcriptomics module then you can call on their tech support to provide assistance as needed. You could do the same with Galaxy but then you will be relying on community support that may not be as prompt or complete as you expect/need.
Thank you so much.