Hi,
I have a list of hits from a magicblast run against a fastq file I have. I was wondering if there is a way to annotate the hits I get. The run was done against nt DB.
The list of hits looks like that:
NB500982:283:HH3WJAFX2:1:21210:15709:8224 gi|1040217674 100 0 0 0 1...
NB500982:283:HH3WJAFX2:1:21210:20062:8227 gi|1040160167 100 0 0 0 1...
NB500982:283:HH3WJAFX2:1:21210:4790:8228 gi|1040197389 100 0 0 0 1...
NB500982:283:HH3WJAFX2:1:21210:12133:8228 gi|164790 98.6667 0 0 0 1...
The gene ID is in the second column.
Thanks
Assa
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written
by
Assa Yeroslaviz
Using EntrezDirect:
$ more gi
1040217674
1040160167
1040197389
$ for i in `cat gi`; do printf ${i}"\t"; esearch -db nuccore -query ${i} | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name,Description,ScientificName; done
1040217674 PROKR2 prokineticin receptor 2 Oryctolagus cuniculus
1040160167 CCDC180 coiled-coil domain containing 180 Oryctolagus cuniculus
1040197389 SORCS1 sortilin related VPS10 domain containing receptor 1 Oryctolagus cuniculus
thanks, I was just now looking into efetch and esearch and tried to concatenate a pipeline for that. but you beat me to it. Thnaks again
Hi again, I'm not sure what elink should do, but with it in the command I don't get any results.
$ esearch -db nuccore -query 34809228 | elink -target gene | esummary | xtract -pattern DocumentSummary -element Id,Caption,Organism
Here I get no results, but with this
$ esearch -db nuccore -query 34809228 | esummary | xtract -pattern DocumentSummary -element Id,Caption,Organism
34809228" term="34809228 AY386695 rabbit
You should have stayed away from GI numbers (if you had that option when you did your magicblast). gi numbers are deprecated for end-user use and this may be one of those examples where things don't work. We can get a result searching with that on NCBI site but the command line query does indeed not seem to be working reliably.
Yes, this is true, but we have to work with what we got. And I got stuck with the gi numbers :-(
So I need to make the best out of it. I don't think magicblast can output something else. But thanks for the help.
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what exactly do you mean with 'annotate'? like get the description line of each hit ?
Yes, I would like to get the gene name and organism.
after looking into the 'manual' of magicblast I don't think you can get that directly from the magicblast output.
You can however run all the hit IDs through entrez or such and retrieve the description for them.
I know I can't get it via
magicblast. My question is how I can get it otherwise.