Question: about annotate transcriptome
gravatar for Kurban
3.6 years ago by
Kurban160 wrote:

i have a transcriptome which include more than 140000 sequences.i wanna annotate them, and someone recommended me to use blast2go, which is really good tool. i tried cloudblast, but did not finish the mini part of the job  the free competition units were used up; then i tried to blast it stopped after a while(after annotated like 100 sequences), sometimes it even report " Problem sending data to the NCBI BLAST server: null. Check Blast Mode: blastX, blastP, etc.", but i think it is not problem of the blast mode, because sometimes that works fine. it is like 40 hours i have been struggling with this.
please give me some suggestions? is there any better way i can get my transcriptome annotated, like i can down load nr database to my laptop do the local blast using blast2go or something else?
i am new at this .

annotation • 1.2k views
ADD COMMENTlink written 3.6 years ago by Kurban160

My guess is that NCBI BLAST is blocking your IP because of too many requests. Many web-servers use a system to protect themselves against automated requests which could overload the server. Depending whether your transcriptome is known (human, mouse, etc) or unknown, there are many tools which align reads onto a reference or de novo. I have used STAR and tophat before and believe these are two of the more commonly used tools for aligning RNAseq reads onto a reference. There are also tools for "de novo transcriptome assembly", for example trinity

ADD REPLYlink written 3.5 years ago by lkmklsmn810
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