User: r.t.greenblatt

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Posts by r.t.greenblatt

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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... OK. So I could combine them using cat in a linux system? ...
written 13 days ago by r.t.greenblatt0
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... OK... As ncRNA are transcribed, I would assume they were in the cdna.all file... and that the folder with the ncRNA, was if someone wanted to just look at ncRNA... The problem is I am interested in both coding and non-coding.... Is there a way to verify that the cdna.all doesn't include ncRNA before ...
written 13 days ago by r.t.greenblatt0
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Hi Johannes, I indeed used the package you provided for my annotations when importing salmon results using txiimport; however, I am receiving very few ncRNA. As I used the cdna.all ensembl file, I can't think why the ncRNA would not be included in my index, as well as in the package you sent... any ...
written 13 days ago by r.t.greenblatt0
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Comment: C: Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
... I have a few ;)  First of all, have you looked at non-coding RNA? These are transcripts that are transcribed (hence RNAseq) but not translated. A lot of the downstream analysis in the vignette is about protein analysis, no?  Also, I am still having difficulties with the switchAnalyzeRlist, as you ...
written 4 weeks ago by r.t.greenblatt0
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Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
... Hi, I am looking to do some downstream analysis on salmon output for non-coding RNA and I would like to look at transcript levels.. I am aware of the option of wasabi --> sleuth, but I was wondering if anyone has tried directly to use IsoformSwitchAnalyzeR or TSIS with transcript counts/abundance ...
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Thanks! I didn't realize that the EnsDb does not include transcript versions, the ignoreTxVersion = TRUE did the trick. I will continue with the analysis as suggested in the vignette.   ...
written 4 weeks ago by r.t.greenblatt0
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Hi Johannes,  Thank you so much for providing the link to the latest EnsDb package.  I am trying to analyze some salmon quantification files, and since I used the transcript annotation files from here (release 92) ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna ...
written 5 weeks ago by r.t.greenblatt0
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Comment: C: Chromosme Name: "CHR_HSCHR19..."
... I understand it is a patch, so if we parse "CHR_HSCHR16_CTG2" we can understand it is from Chr 16?  ...
written 12 weeks ago by r.t.greenblatt0
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Chromosme Name: "CHR_HSCHR19..."
... Hi, I have requested a biotype from biomart in the "attributes" section, and some of the results are returned with this style chromosome name "CHR_HSCHR19_2_CTG2". How can I correct this?    library(biomaRt) #get annotations for processed transcripts mart <- biomaRt::useMart( biomart = "E ...
biomart ensembl grch38 written 12 weeks ago by r.t.greenblatt0
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Comment: C: Scan error using biomart with version option
... I am having the same issue....have anyone come up with a solution?  ...
written 12 weeks ago by r.t.greenblatt0

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