Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • CanFam2 data RNAseq samples and GenomicRanges

    hi All,
    I am processing RNAseq samples for canFam2. I used the following commands from GenomicRanges package that gives me only 1218 genes. (because by default refGene for canFam2 retains only known genes.)

    txdb <- makeTranscriptDbFromUCSC(genome = "canFam2", tablename = "refGene")
    TranscriptDb object:
    | Db type: TranscriptDb
    | Data source: UCSC
    | Genome: canFam2
    | UCSC Table: refGene
    | Type of Gene ID: Entrez Gene ID
    | Full dataset: yes
    | transcript_nrow: 1218
    | exon_nrow: 11256
    | cds_nrow: 10922
    | Db created by: GenomicFeatures package from Bioconductor
    | Creation time: 2011-08-08 12:56:52 -0400 (Mon, 08 Aug 2011)
    | GenomicFeatures version at creation time: 1.4.2
    | RSQLite version at creation time: 0.9-4
    | DBSCHEMAVERSION: 1.0

    To get all the genes, I changed the table name to "xenoRefGene" but that does not fetch the "gene Ids". Also, the number of transcripts (229403) looks abnormally large.

    TranscriptDb object:
    | Db type: TranscriptDb
    | Data source: UCSC
    | Genome: canFam2
    | UCSC Table: xenoRefGene
    | Type of Gene ID: no gene ids
    | Full dataset: yes
    | transcript_nrow: 229403
    | exon_nrow: 1110585
    | cds_nrow: 747878
    | Db created by: GenomicFeatures package from Bioconductor
    | Creation time: 2011-08-08 12:51:29 -0400 (Mon, 08 Aug 2011)
    | GenomicFeatures version at creation time: 1.4.2
    | RSQLite version at creation time: 0.9-4
    | DBSCHEMAVERSION: 1.0


    please help.

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 07:23 AM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-17-2024, 06:54 AM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-13-2024, 08:58 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Working...
X