User: doinelpierrot

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Posts by doinelpierrot

<prev • 12 results • page 1 of 2 • next >
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Comment: 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 doinelpierrot0
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Comment: 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 doinelpierrot0
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From accession ID to phylum taxid
... 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 ...
rna-seq written 2 days ago by doinelpierrot0 • updated 1 day ago by shenwei3565.5k
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R cannot delete tmp file
... 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 ...
R written 2 days ago by doinelpierrot0
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Comment: C: From accession ID to phylum taxid.
... 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 doinelpierrot0
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Comment: C: Accession id to taxid
... Hope it's more understandable now ! ...
written 9 days ago by doinelpierrot0
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Comment: C: How percentage of identity is calculated ?
... 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 doinelpierrot0
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How percentage of identity is calculated ?
... 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 ...
alignment written 13 days ago by doinelpierrot0
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Comment: C: Good bowtie2 alignment rate and low mapping on transrate ...
... 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 doinelpierrot0
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Good bowtie2 alignment rate and low mapping on transrate ...
... 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 ...
software error assembly rna-seq written 22 days ago by doinelpierrot0 • updated 21 days ago by Istvan Albert ♦♦ 85k

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