Comments (3)
Heya @eul2021,
Yeah maybe the simplest option is to try the SRA website and slap an OR
between each SRR accession code as your search query. Like this: https://www.ncbi.nlm.nih.gov/sra/?term=ERR3569471++OR+ERR3569472 (maybe break this down into 250 accession chunks).
If that returns the query you want click on "Send To: --> File --> SraRunInfo" and you get a simple table of the results.
You can try the SRAdb
package
Finally you can login to the Serratus SQL server and we have a table called srarun
which contains the standard SRA meta-data for all the runs we have analyzed.
from serratus.
Oh and this might be a great time for me to plug palmID
, this is an experimental RdRP interface for the Serratus data which pulls SRA meta-data automatically. From the RdRP reports here you can download the meta-data directly as a CSV. It doesn't work for a whole family though, you input a single sequence and it will pull down all matches down to ~40% identity in the RdRP. This is a more conservative analysis, but has good specificity for RNA viruses which can be subsequently assembled.
from serratus.
Artem, thank you very much for a quick response and for useful suggestions! I'll try all of them:-)
from serratus.
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from serratus.