Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • h_manoj
    started a topic htseq read counts different in separate runs

    htseq read counts different in separate runs

    Hello,

    I had used tophat2 to map a set of fastq files. I noticed that the reads mapped for some features were different in two separate runs (for eg., ENSMUSG00000047905 produced 4335 reads in one run while it shows only 2 reads in another run), even though I had kept all options constant in both runs. The only change was the annotation file. In the first try, I used the gencode M2 gtf file which contained only level 1 and level 2 features. In the second trial, I had used the complete gtf file. But, the feature (ENSMUSG00000047905) that I am checking has no difference in either annotation files.

    Details of ENSMUSG00000047905 in gencode level 1 and level 2 annotation file:
    login3$ grep ENSMUSG00000047905 gencode.vM2.annotation.gtf |grep -w gene
    chr6 HAVANA gene 67205619 67206083 . + . gene_id "ENSMUSG00000047905.10"; transcript_id "ENSMUSG00000047905.10"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "Gm8566"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "Gm8566"; level 2; havana_gene "OTTMUSG00000024710.1";

    Details of ENSMUSG00000047905 in gencode complete annotation file:
    login3$ grep ENSMUSG00000047905 gencM2_levels1and2.gtf |grep -w gene
    chr6 HAVANA gene 67205619 67206083 . + . gene_id "ENSMUSG00000047905.10"; transcript_id "ENSMUSG00000047905.10"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "Gm8566"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "Gm8566"; level 2; havana_gene "OTTMUSG00000024710.1";
    login3$

    What would be the reason for this? Is this expected? Appreciate any help!
    Thanks.
    Last edited by h_manoj; 02-06-2014, 12:42 PM.

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, Yesterday, 07:49 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-20-2024, 07:23 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-17-2024, 06:54 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Working...
X