Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • roll
    replied
    When i do the above, i tried to upload it to UCSC genome browser as custom track but it says it cant read my bigwig file.
    I converted my bigwig to wig, this time it gives memory error.

    Any ideas why this might be happening? or how to fix it?

    Leave a comment:


  • roll
    replied
    Originally posted by id0 View Post
    There are several options. I use bedtools genomeCoverageBed to convert from BAM to BedGraph. Then bedGraphToBigWig to convert BedGraph to BigWig.

    Maybe someone else knows of a single step option.
    This is chip-seq data and i used the following commands

    1. bedtools genomecov -bg -ibam Mysorted.bam > Mysorted.bedGraph

    2. bedgraphToBigWig in.bedGraph chrom.sizes out.bw

    At step 2, I am not sure if I understand what is the chrom.sizes file is. Shall i just create one myself simply subtracting end position from the start position to create the chrom.sizes?
    I guess 'in.bedGraph' is my Mysorted.bedGraph.

    Am i missing something?

    Leave a comment:


  • Wallysb01
    replied
    if this is RNA-seq data, be sure to use the -splice option for genomeCoverageBed

    Leave a comment:


  • lindenb
    replied
    I wrote a Bam2wig : https://github.com/lindenb/jvarkit/wiki/Bam2Wig
    It use the cigar elements to get the depth.

    ( however, I did not often used it)

    Leave a comment:


  • id0
    replied
    There are several options. I use bedtools genomeCoverageBed to convert from BAM to BedGraph. Then bedGraphToBigWig to convert BedGraph to BigWig.

    Maybe someone else knows of a single step option.

    Leave a comment:


  • roll
    started a topic How to convert sam/bam or bed file into wig file

    How to convert sam/bam or bed file into wig file

    Hi,

    How what tools can I use to convert sam/bam or bed file into a wig file?

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 02:20 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
181 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:18 AM
0 responses
228 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-06-2024, 08:04 AM
0 responses
184 views
0 likes
Last Post seqadmin  
Working...
X