Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • lh3
    replied
    It should work, but will be very slow.

    Leave a comment:


  • lre1234
    replied
    I can also get the command that you have to work fine. But I have been trying to get this to work with using the '-L MyRegions.bed' samtools command to get multiple regions from a bed file, but it doesn't seem to work. Is that not allowed with using the ftp file?

    Leave a comment:


  • GenoMax
    replied
    There must be some sort of restriction (firewall?) for using ftp on your cluster node. I did get a output file using your command. Output is in SAM format BTW, using your command.
    Last edited by GenoMax; 10-15-2014, 04:59 AM.

    Leave a comment:


  • marco12345
    started a topic Download bam region from 1000 genome project

    Download bam region from 1000 genome project

    Hi,

    I am trying to download only one (or more) region from a bam file from the 1000 Genome Project without having to download the whole file.
    The way the 1000GP website suggests seems not to work for me, and I can't pinpoint the problem. Could you please help me?

    I am working on a cluster using Linux.
    Here's the command I sent:
    samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...e.20120522.bam 17:41243452-41277500 > HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.chr17reg1.bam

    The resulting file is an empty bam with no header.

    Thanks!
    Last edited by marco12345; 10-15-2014, 01:54 AM.

Latest Articles

Collapse

  • seqadmin
    Quality Control Essentials for Next-Generation Sequencing Workflows
    by seqadmin




    Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

    Nucleic Acid Quality Control
    Preparing for NGS starts with isolating the...
    02-10-2025, 01:58 PM
  • seqadmin
    An Introduction to the Technologies Transforming Precision Medicine
    by seqadmin


    In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
    01-27-2025, 07:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 02-07-2025, 09:30 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-05-2025, 10:34 AM
0 responses
101 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-03-2025, 09:07 AM
0 responses
81 views
0 likes
Last Post seqadmin  
Started by seqadmin, 01-31-2025, 08:31 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Working...
X