User: neranjan

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neranjan20
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New User
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US
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2 months, 3 weeks ago
Joined:
2 years, 10 months ago
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Posts by neranjan

<prev • 23 results • page 1 of 3 • next >
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Comment: A: a problem while using fastq-dump to split SRR files
... looks like you are out of space in your working $HOME space. To check the usage / amount of space you have, you can may be you can use; quota --local-only To check how much you have used try: du -h ...
written 12 weeks ago by neranjan20
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Comment: A: Link mice RNA-seq data to proteins
... I think you can use Tuxedo suite can be use to analyze RNA Seq data. [Tuxedo suite][1] includes: Bowtie, tophat, cufflinks , these can be also implement using Galaxy platform if you are not familiar with command line tools. Now there are new tools that can be included as well, which HISAT2-Stringti ...
written 3 months ago by neranjan20
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Comment: A: Link mice RNA-seq data to proteins
... There are many pipelines that can do the analysis, and if you want to create a custom pipeline you can check out [Galaxy website][1]. [1]: https://usegalaxy.org/ ...
written 3 months ago by neranjan20
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Answer: A: Extract reads used for contigs assembly
... how about using **quast** software to get a analysis report on the assembly [http://quast.sourceforge.net/quast][1] [1]: http://quast.sourceforge.net/quast ...
written 3 months ago by neranjan20
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Comment: C: How to add biological annotations using R
... Thanks, I think i was looking at more of **only** saving the ensemble database, and I think it can be done using: rat_ensembl = useDataset("rnorvegicus_gene_ensembl",mart=ensembl) save(rat_ensembl, file = "rat_ensembl.RData") Then loading using: load("rat_ensembl.RData") ...
written 3 months ago by neranjan20
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Comment: C: How to add biological annotations using R
... not the assignment operator !!! What I meant is to save it as object for later use, so I can load it when I do need it. (since these versions change what they have with time) So is there a way to save this object in my hard drive? (some sort of similar way as they do in TxDb objects) samplef ...
written 3 months ago by neranjan20
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Answer: A: How to add biological annotations using R
... en_2=useMart("ensembl", host = "http://feb2014.archive.ensembl.org") human_2 = useDataset("hsapiens_gene_ensembl",mart=en_2) So as a last question to close this , is there a way to save this "mart" object for later use. (or as a reference for later analysis) ? ...
written 3 months ago by neranjan20
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Comment: C: How to add biological annotations using R
... Thanks @swbarnes2 and @b.nota I was able to replicate the NOISeq data length using a older version of mart, and also using transcript start and end locations to calculate the length. So my final code would be: en_2=useMart("ensembl", host = "http://feb2014.archive.ensembl.org") human_2 = ...
written 3 months ago by neranjan20
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Comment: C: How to add biological annotations using R
... it is possible, but in `NOISeq` it does not say which it is been using. But again, the difference is **huge**, so it is obvious that I am missing something in calculating the gene-length. I also tried to calculate the mean, median and sum of transcript length, and which was way off than the numbe ...
written 3 months ago by neranjan20
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Comment: A: How to add biological annotations using R
... Thank you I was able to use `biomaRt` package to grab the required sequences using: g_ids=c("ENSG00000177757", "ENSG00000187634", "ENSG00000188976") human <- useMart("ensembl", dataset="hsapiens_gene_ensembl") gene_coords=getBM(attributes=c("ensembl_gene_id", "start_position","end_po ...
written 3 months ago by neranjan20

Latest awards to neranjan

Scholar 8 months ago, created an answer that has been accepted. For A: HISAT2 Indexing using annotation for Rattus_norvegicus

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