Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • coverageBed using paired-end fastq as input

    I am new to Illumina data with more experience with Ion Torrent data. Recently, I have some fastq files and before:

    CoverageBed using a bam:
    Code:
     coverageBed -d -a targets.bed -b IonXpress_.bam > IonXpress_output.txt

    Now that I have 2 paired-end fastq files:
    S5_R1.fastq
    S5_R2.fastq

    How do I use them with coverageBed? Thank you .

  • #2
    And you are back

    You seem to have overlooked the step of having to trim/align the fastq files to get an alignment file (BAM) before you can think about coverageBed.

    Comment


    • #3
      I am totally new to Illumina data and admit I did not think of that step. Do you have any recommendations far as what to use or where to begin? Thank you .

      Comment


      • #4
        Originally posted by cmccabe View Post
        I am totally new to Illumina data and admit I did not think of that step. Do you have any recommendations far as what to use or where to begin? Thank you .
        What kind of data is this? I will suggest starting with BBDuk (to trim data/look for adapters) and then BBMap (to align) but other aligners will work as well.

        Comment


        • #5
          This is Illumina paired-end data from a NextSeq. I will give those to applications a try. Thank you .

          Comment


          • #6
            Originally posted by cmccabe View Post
            This is Illumina paired-end data from a NextSeq. I will give those to applications a try. Thank you .
            Is it DNAseq, RNASeq, ChIP_seq .. "what-seq" kind of data. BBMap would work for all of those but downstream analysis will be different.

            Comment


            • #7
              It is DNA-seq data. Thank you .

              I spent some time reading and learning some programing. Thank you for your helpful posts
              Last edited by cmccabe; 10-28-2015, 02:34 PM.

              Comment

              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, 07:23 AM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 06-17-2024, 06:54 AM
              0 responses
              11 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 06-14-2024, 07:24 AM
              0 responses
              24 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 06-13-2024, 08:58 AM
              0 responses
              17 views
              0 likes
              Last Post seqadmin  
              Working...
              X