I am preparing for doing a comparative transcriptome analysis and would like to know which are the skills I should try and work on before getting the data. Which kind of coding program would be more useful to learn? Any articles with pipelines you can recommend? Other programs widely used? Anything other than computing abilities that may come handy?
First, I recommend to figure out what you want to analyze. For example, transcriptome data can be used for improving gene predictions, for checking which transcripts are expressed to what extent, for comparing transcription in different samples of the same species, or even between different species.
Once you have figured that out, look for a recent review in that particular field, read what software is currently recommended. Also look at recent publications and preprints that performed similar analysis, check which software did those authors use (might be more recent than something in a review).
Then download and install that software, hopefully it comes with a toy data set to play with. If not, download test data from NCBI genomes & SRA (you can shrink both data sets, e.g. by restricting your analysis to part of a chromsome or the transcripts there, and to reads that map to that part of chromsome instead of the full library).
I believe bash/unix skills are extremely useful in addition to learning how to use some specific software.
Software that I personally found useful:
RNA-Seq quantification for comparing different samples from the same species: kallisto & R
RNA-Seq to genome mapping: hisat2
RNA-Seq aided genome annotation: BRAKER/AUGUSTUS/GeneMark-ET
First, I recommend to figure out what you want to analyze. For example, transcriptome data can be used for improving gene predictions, for checking which transcripts are expressed to what extent, for comparing transcription in different samples of the same species, or even between different species.
Once you have figured that out, look for a recent review in that particular field, read what software is currently recommended. Also look at recent publications and preprints that performed similar analysis, check which software did those authors use (might be more recent than something in a review).
Then download and install that software, hopefully it comes with a toy data set to play with. If not, download test data from NCBI genomes & SRA (you can shrink both data sets, e.g. by restricting your analysis to part of a chromsome or the transcripts there, and to reads that map to that part of chromsome instead of the full library).
I believe bash/unix skills are extremely useful in addition to learning how to use some specific software.
Software that I personally found useful:
RNA-Seq quantification for comparing different samples from the same species: kallisto & R
RNA-Seq to genome mapping: hisat2
RNA-Seq aided genome annotation: BRAKER/AUGUSTUS/GeneMark-ET
Hi,
You first need to be clear regarding your objective from the work. I completely agree with Katharina Hoff. Apart from her suggestions you should learn about the different file formats involved in transcriptome analysis and the you should focus upon a programming language,alternatively there are GUI based tools available as well. Galaxy is pretty good to use as well, being free is a huge bonus as well.
Hope this helps.
Best Wishes
Pankaj
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