Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • other problems with tophat 1.1.3

    I tried running my SOLiD reads on Tophat 1.1.3 after they exited due to a bug from 1.1.2 last night only to get the following error message:

    [Tue Nov 16 16:58:40 2010] Beginning TopHat run (v1.1.3)
    -----------------------------------------------
    [Tue Nov 16 16:58:40 2010] Preparing output location /r/solid_xfer/Internal/AD/M_KOHLI/AD6/Analysis/TopHat_8//
    [Tue Nov 16 16:58:40 2010] Checking for Bowtie index files
    [Tue Nov 16 16:58:40 2010] Checking for reference FASTA file
    [Tue Nov 16 16:58:40 2010] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Tue Nov 16 16:58:40 2010] Checking for Samtools
    Samtools version: 0.1.8.0
    [Tue Nov 16 17:03:01 2010] Checking reads
    min read length: 50bp, max read length: 50bp
    format: fasta
    here was my input:
    /tophat -C --quals -o /r/TopHat_8 --library-type fr-secondstrand -p 8 /hg18_c_index/hg18_c /r/reads.csfasta /r/reads.qual


    Can anyone tell me what could possibly be wrong. I ran the same line on v1.1.2 and it ran until the bug in the program made it stop.

    Thanks in advance.

    Zorph

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, 07-19-2024, 07:20 AM
0 responses
32 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
54 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X