User: doinelpierrot
doinelpierrot • 0
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Posts by doinelpierrot
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C: From accession ID to phylum taxid
... Ok thanks ! I'm open to new tools too. i have checked Blobtools doc (https://blobtools.readme.io/docs/taxify). But I haven't use it before and I don't really get exactly how to use my data with it ...
written 1 day ago by
doinelpierrot • 0
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C: From accession ID to phylum taxid
... Thanks for your advice, you are right. Then the best for me would be to have the full information like for each lvl, the result (for instance "human" fo species or "Non assigned" if not found) but I don't know how to do that.
Or a less ambitious way would be to get the phylum with "grep phylum", ...
written 2 days ago by
doinelpierrot • 0
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... Hello guys,
I have a list of 10 000 accessions id from blast in a txt file (XP_002184977.1 GBG35237.1) and I would like to have the taxonomy associated (in a tab file that correpond to my accessions line per line). So I'm using Entrez direct like this :
esearch -db protein -query "XP_002184977 ...
written 2 days ago by
doinelpierrot • 0
• updated
1 day ago by
shenwei356 ♦ 5.5k
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... Hello guys,
I am using R and more precisely the library taxonomisr to analyse some data. However I have an error message when running :
*taxaId<-accessionToTaxa(c("LN847353.1","AL079352.3"),"accessionTaxa.sql")*
The error is :
Warning messages:
1: In file.remove(tmp) :
impossible to delete ...
written 2 days ago by
doinelpierrot • 0
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... Thank you so much ! I am definitively trying that !
(It is better than BBMA Pthat does not give you the phylum taxid, but for those who still want to use BBMAP the new files are in ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/ .) ...
written 9 days ago by
doinelpierrot • 0
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C: Accession id to taxid
... Hope it's more understandable now ! ...
written 9 days ago by
doinelpierrot • 0
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... Thanks for your help ! I'm a bit confused since I have specified **-maxhsps 1** in my command and somehow I sometimes get result >100 in the column HSP_identity, more especialy when the HSP e-value is low.
EDIT : I found the answer of my question : on plast, percentage identity = HSP_identity / ...
written 13 days ago by
doinelpierrot • 0
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... Hello all,
I'm using Plastx (some faster equivalent of Blastx) to compare my 500k contigs to ncbi database in order to check some suspected unknown contamination. I would like to only select the results with a percentage of identity > 95%. However there is no such "percentage identity colum" in ...
written 13 days ago by
doinelpierrot • 0
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... Ok so I have many reads that map different places of my transcriptom. I know I had a lot of duplicates in my reads. Could it be an explanation ? ...
written 21 days ago by
doinelpierrot • 0
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... Hello everybody !
I've run my first assembly recently and I'm trying to figure out its quality. I have honest n50 and a not so bad BUSCO of 80% complete busco. However, I am receiving mixed signals from Transrate and Bowtie2.
For both of them I have sent as input my trimmed fastq files and my fina ...
written 22 days ago by
doinelpierrot • 0
• updated
21 days ago by
Istvan Albert ♦♦ 85k
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