Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • HTseq-count errors

    I put 10 .bam files (from Tophat) through the same samtools & htseq-count commands, and 3/10 didn't work (each with their own error) in htseq.

    $ samtools view -h -o sample.sam sample.bam

    $ htseq-count --stranded no -i gene_id sample.sam genes.gtf > sample.gene.counts

    The errors are:

    1) ...596437 GFF lines processed.
    Error occured when reading beginning of SAM/BAM file.
    [Exception type: StopIteration, raised in count.py:84]

    This one particularly confuses me since the program didn't choke on any of the other sam files that were prepared the same way.

    2) ...20000000 SAM alignment records processed.
    Error occured when processing SAM input (line 20080682 of file TH2/DEprep/BR2_N2In.sam):
    ('SAM line does not contain at least 11 tab-delimited fields.', 'line 20080682 of file TH2/DEprep/BR2_N2In.sam')
    [Exception type: ValueError, raised in _HTSeq.pyx:1276]

    3) ...35089676 SAM alignments processed.
    [Errno 5] Input/output error
    [Exception type: IOError, raised in count.py:212]


    Any suggestions for how I should fix these problems?

  • #2
    I wonder if you're having hard drive corruption issues.

    In any case, make sure you're using the most recent version of htseq-count. Also, check line 20080682 of the sam file mentioned and ensure it's not malformed.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin


      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
      Today, 07:01 AM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    37 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    39 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    34 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    54 views
    0 likes
    Last Post seqadmin  
    Working...
    X