Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to customize cufflinks output COLUMNS

    Hi-
    I am running cufflinks on mouse RNAseq with genes.gtf as reference file on the bam files that i generated using tophat2/bowtie. The output genes.fpkm_tracking and isoforms.fpkm_tracking have the following format:
    tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status
    ENSMUSG00000090025 - - ENSMUSG00000090025 Gm16088 TSS82763 1:3054232-3054733 - - 0 0 0 OK
    ENSMUSG00000064842 - - ENSMUSG00000064842 Gm26206 TSS81070 1:3102015-3102125 - - 0 0 0 OK
    ENSMUSG00000025900 - - ENSMUSG00000025900 Rp1 TSS11475 1:4343506-4360314 - - 0 0 0 OK

    However, I also want the column that enlists the gene biotype (pseudogene, protein coding..) that is in the gtf file i am using as reference. how can I incorporate this in the run? is it doable? I'd appreciate the help in this matter.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 11:09 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
148 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
122 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
111 views
0 likes
Last Post seqadmin  
Working...
X