Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • bigblackbox
    Junior Member
    • May 2020
    • 2

    #1

    What is the Bowtie2 default output file extension?

    I'm processing samples for atac-seq using this galaxy tutorial (https://galaxyproject.github.io/trai...l.html#mapping) and I ran this command line:

    bowtie2 --dovetail --very-sensitive -X 1000 -k 10 -x /user/mm10/mm10 -1 /user/Cutadapt_res/p4/p4_wt_r1.fastq.gz -2 /user/Cutadapt_res/p4/p4_wt_r2.fastq.gz

    I got two output files:

    Discover the magic of the internet at Imgur, a community powered entertainment destination. Lift your spirits with funny jokes, trending memes, entertaining gifs, inspiring stories, viral videos, and so much more from users.


    Are these the correct output files I should be getting? Both output files, .e2546134 and .o2546134 doesn't have a extension but the .e2546134 file is openable with a text edit program and shows the alignment info so I assumed the bowtie2 command worked and everything ran and completed.

    I want to run the .o2546134 into samtools but before I do that, do I need to manually add in the extension and make it bowtie2_p1.e2546134.bam?


    Sorry if this is a common question, it's my first time doing this analysis and I couldn't google the answer.

    Thanks,

Latest Articles

Collapse

  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2




    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
    Yesterday, 06:46 AM
  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
29 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-28-2026, 09:51 AM
0 responses
18 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 11:13 AM
0 responses
71 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-22-2026, 10:48 AM
0 responses
48 views
0 reactions
Last Post SEQadmin2  
Working...