Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • HTSeq problem on Windows

    Hi, I would appreciate any hints anyone might have on this one.

    I am trying to get HTSeq-count to work on my Windows 7 machine in order to prepare data for DESeq. Installation went fine, but whenever I try to run it, it processes all the lines in my GFF file and then a pop-up window comes up saying "python.exe has stopped working. A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available"

    Right before this pops up, it says "Warning: Malformed SAM line: RNAME != '*' although flag bit &0x004 set". But in my searches on this forum, people seem to say this warning can usually be ignored, so I'm not sure it's related to my problem, besides indicating that HTSeq has gotten to the step of processing the SAM file before causing the problem.

    I've tried this on a couple different SAM files form different sources (that were name-sorted as BAM files and then converted to SAM using SAMtools) and the same error always pops up. My GTF file is the human file from Ensembl. Any ideas? Is this most likely a problem with HTSeq, my installation, or even my machine? I don't know where to look.

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
32 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Working...
X