Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bowtie: extra parameter error

    I'm trying to execute

    Code:
    bowtie –m 1 -S /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam
    but I'm getting

    Code:
    Extra parameter(s) specified: "whole_sample.fastq", "whole_sample.sam"
    This is quite annoying and I am sure there is some stupid syntax error on my part. Can you help spot it? This is bowtie version 1.0.

    --EDIT: I reversed the place of the parameters:

    Code:
    bowtie -S -m 1  /hts/galaxy/data/references/genomes/mus-musc/ens73/mm73 whole_sample.fastq whole_sample.sam
    and now it works. This is bizarre. Apparently, the sequence of the parameters makes a difference but it is not something I find obvious from the bowtie manual.
    Last edited by feralBiologist; 11-21-2013, 06:09 AM.

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
22 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
19 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Working...
X