Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • read count with multicov

    Hi,

    I am doing a gene expression analysis, I have a raw data of libraries of RNAseq (microRNAs) of 2 conditions and 11 replicates each one, I used multicov to obtain the reads count

    bedtools multicov -bams SRR1054203.gz.segemehl.sam.bam.sorted.bam.bam SRR1054204.gz.cutadapt204.cutadapt.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054205.gz.cutadapt205.cutadapt.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054206.gz.cutadapt206.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054207.gz.cutadapt207.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054208.gz.cutadapt208.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054209.gz.cutadapt209.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054210.gz.cutadapt210.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054211.gz.cutadapt211.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054212.gz.cutadapt212.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054218.gz.cutadapt218.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054217.gz.cutadapt217.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054213.gz.cutadapt213.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054214.gz.cutadapt214.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054215.gz.cutadapt215.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054219.gz.cutadapt219.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054220.gz.cutadapt220.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054221.gz.cutadapt221.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054222.gz.cutadapt222.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054223.gz.cutadapt223.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054224.gz.cutadapt224.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054225.gz.cutadapt225.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054226.gz.cutadapt226.fastq.segemehl.sam.bam.sorted.bam.bam SRR1054216.gz.cutadapt216.fastq.segemehl.sam.bam.sorted.bam.bam -bed results.out > conteo_mature_genome2

    the result

    chr20 62550849 62550871 hsa-mir-941-1 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550905 62550927 hsa-mir-941-2 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550961 62550983 hsa-mir-941-2 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551156 62551178 hsa-mir-941-2 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551268 62551290 hsa-mir-941-2 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550905 62550927 hsa-mir-941-3 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550961 62550983 hsa-mir-941-3 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551156 62551178 hsa-mir-941-3 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551268 62551290 hsa-mir-941-3 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550905 62550927 hsa-mir-941-4 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550961 62550983 hsa-mir-941-4 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551156 62551178 hsa-mir-941-4 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551268 62551290 hsa-mir-941-4 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550905 62550927 hsa-mir-941-5 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62550961 62550983 hsa-mir-941-5 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551156 62551178 hsa-mir-941-5 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37
    chr20 62551268 62551290 hsa-mir-941-5 hsa-miR-941 MIMAT0004984 Homo sapiens miR-941 17 7 12 42 23 41 40 31 28 35 584 45 49 14 53 198 72 7 43 54 37 93 44 37

    I found for example, several time the mature hsa-miR-941 MIMAT0004984 with different hairpin names and some of them have the same coordinates, and they have the same number of reads count.

    I do not know if it possible to have the option of a window to aggregate nucleotides in order to merge read that starts with a few nucleotides of differences, but that belong to the same mature microRNA and report only one microRNA ID.

    I check the bedtools manual and have the windowsbed but with multicov it does not work, any idea?. I need to overcome this because when I use this table in edgeR or DESeq, it does not work with repeated ID:

    Thanks very much

    regards

    Adriana

  • #2
    You can download from miRBase a file with only the mature miRNAs.

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      05-06-2024, 07:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Today, 01:32 PM
    0 responses
    4 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-24-2024, 07:15 AM
    0 responses
    198 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    220 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    229 views
    0 likes
    Last Post seqadmin  
    Working...
    X