Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • combining htseq-count files into one

    Hi.
    I have 12 htseq-count result files.
    When I tried to combine them with Excel, I found that there were some missing rows in one file that were present in another.
    For example,
    <file1>
    a1 3
    a2 4
    a3 5
    a4 3

    <file2>
    a1 4
    a3 6
    a4 5


    Hot can I combine without loss of data like following?
    <file 1+2>
    a1 3 4
    a2 4 N/A
    a3 5 6
    a4 3 6


    Thank you!

  • #2
    1. If there are missing rows, then you have a prime example for a data manipulation that is trivial in any statistics or scripting language but really complicated in Excel. Time to learn some scripting.

    2. There shouldn't be any missing rows, because htseq-count outputs a count for each gene that is mentioned with an exon line in the GTF file, no matter whether reads map to it or not. Something went wrong. Maybe you used different annotation files?

    Comment


    • #3
      Thanks for the reply.
      I'm actually learning python now, but it is difficult learn it since no one around me is familiar with scripting.
      Anyway, I ran htseq-count with SAM and GTF files for each sample.
      Following is the command I used for it.
      htseq-count -m intersection-strict -s no -i gene_naem I1.sam /home/bk/Desktop/bosTaurus_2013/GTF/I1_transcripts.gtf > I1_counts.txt
      I have data from 12 different samples, so I changed the file names according to the sample names.

      Comment


      • #4
        Are these de novo assemblies or did you make a gtf file for each sample using Cufflinks? Because it looks like you are using a gtf file specific to the sample.

        In that case, each gtf will have slightly different lists of transcripts. In order to have htseq-count give the same output for each sample, you need to use the same gtf file for all of them.

        Comment


        • #5
          I didn't make GTF files. They are from a company we paid for sequencing.
          I know the company used Cufflinks for expression estimation.

          They didn't really explain me about those files. Besides I don't have much knowledge in the bioinfo. area, so everything is confusing for me.

          So what should I do to get the same GTF file

          Sorry for my disorganized question. English is not my primary language, so please understand...

          Comment


          • #6
            Have a look at the cuffmerge command that comes with cufflinks.

            Comment


            • #7
              Not a problem. Use cuffmerge to merge all the GTF files into a into a single GTF and then use htseq-count using the merged GTF file.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Essential Discoveries and Tools in Epitranscriptomics
                by seqadmin


                The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
                Yesterday, 07:01 AM
              • seqadmin
                Current Approaches to Protein Sequencing
                by seqadmin


                Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                04-04-2024, 04:25 PM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 04-11-2024, 12:08 PM
              0 responses
              39 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 10:19 PM
              0 responses
              41 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 09:21 AM
              0 responses
              35 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-04-2024, 09:00 AM
              0 responses
              55 views
              0 likes
              Last Post seqadmin  
              Working...
              X