Hi,
Any pointer (tutorial, review, pipeline examples) on the steps required for the bioinformatic analysis of cDNA data?
Thanks in advance.
First thing to do is to know from which cell type or tissue the mRNA was collected that was copied into cDNA and sequenced to give you the EST data you have. Everything you determine from the sequence itself should be put into the context of that cell or tissue.
Is this raw RNA-seq data? If so, a good first step would be to QC it. FastQC works well for this purpose. Regardless, you probably want to perform some BLASTs to see what is being expressed (and by what organism if you were not given this information). You can also look at some basic statistics such as GC percentage with an eye out for anything unusual.
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version 2.3.6
From Wikipedia "An expressed sequence tag or EST is a short sub-sequence of a cDNA sequence." So you have part of a cDNA. Which means you have an EST.
What do you want to do with your cDNA?
Do you mean cDNA from sequencing a library? I'd say your question to too vague to be interpreted. Can you elaborate a little more?
Hi, I'm so sorry for the vagueness of my question. Yes, I'm actually given a part of a cDNA with its forward and backward sequence that I need to analyse it. I had run blastx to get the translated protein and then blastp it to obtain the protein. Sorry for my ignorance, as I am new to this field and wish to get some advice on how to proceed. Most of the journals I came across is on the analysis of ESTs, but I was wondering if anyone could just give some idea on some analysis for cDNA.