Question: Human Genbank Ids
0
gravatar for Zev.Kronenberg
5.4 years ago by
United States
Zev.Kronenberg11k wrote:

I am working on a sequencing run that contains contamination. I did a de novo assembly and blasted the results against NR and filtered for the best hits. I now have a list of Genbank Ids. I simply want to know which IDs are human so I pull those contigs for further analyses.

Thanks

genbank blast • 1.2k views
ADD COMMENTlink modified 5.4 years ago by deanna.church1.1k • written 5.4 years ago by Zev.Kronenberg11k
2

Hello, Downloading a list of genbank ids (limits - human) from ucsc (table browser) and using fgrep to your list helps?

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by AndreiR240
1
gravatar for deanna.church
5.4 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

Use e-utilities to pull the records and get the taxonomic ids. http://www.ncbi.nlm.nih.gov/books/NBK25500/

taxid 9606 == human

ADD COMMENTlink written 5.4 years ago by deanna.church1.1k

bingo. I knew there was a "right/easy" way.

ADD REPLYlink written 5.4 years ago by Zev.Kronenberg11k
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