Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • fastq to bam

    Hi!
    Can anyone tell me is it possible to convert a .fastq file to a .bam file? How to convert or which tool can I use?
    Thanks in advance.

  • #2
    Yes it is possible to convert a fastq file to BAM but only after you use a suitable alignment tool to align it to a reference.

    Comment


    • #3
      Fastq is raw data (input)...BAM is an alignment file (output)

      One is generated from the other using mapping/ de novo assembly software...One can not simply convert

      Comment


      • #4
        Originally posted by JackieBadger View Post
        Fastq is raw data (input)...BAM is an alignment file (output)

        One is generated from the other using mapping/ de novo assembly software...One can not simply convert
        thank you, could you tell me how to align or map fastq? what tool will you recommend?

        Comment


        • #5
          Originally posted by hugh_hang View Post
          thank you, could you tell me how to align or map fastq? what tool will you recommend?
          See the link I had included in my response in post #2.

          Comment


          • #6
            Use FastqToSam from picard tools. Then convert sam to bam using SamFormatConverter.

            Comment


            • #7
              Originally posted by JackieBadger View Post
              Fastq is raw data (input)...BAM is an alignment file (output)

              One is generated from the other using mapping/ de novo assembly software...One can not simply convert
              Well, you can store unmapped reads in SAM/BAM, so a simple conversion at that level is possible although not what is usually meant (aligning):
              I think it is time to retire the FASTQ file format in favour of storing unaligned reads in SAM/BAM format . I will try to explain, as thi...

              Comment


              • #8
                Hi i am new to NGS analysis. I have read and tried many answers regarding converting fastq to sam through picard tools, But it dnt work out? is there any other way to do that?thank u.

                Comment


                • #9
                  Originally posted by madhavi View Post
                  Hi i am new to NGS analysis. I have read and tried many answers regarding converting fastq to sam through picard tools, But it dnt work out? is there any other way to do that?thank u.
                  I am afraid I don't know more than you do. I just followed them and get something undesirable.

                  Comment


                  • #10
                    You probable need to use a read mapping tool like BWA or Bowtie2 to align the raw FASTQ reads to a genome giving you aligned reads in SAM/BAM format.

                    This is not simply "converting" from FASTQ to SAM/BAM. The tools look at each FASTQ read and search the genome looking to find where it matches best in order to "align" the read to the genome.

                    (I am basically repeating what GenoMax said in his first reply at the start of this thread.)

                    Comment


                    • #11
                      Originally posted by bishwo View Post
                      Use FastqToSam from picard tools. Then convert sam to bam using SamFormatConverter.
                      Hello I seen a script on this link https://code.google.com/p/fasta-to-fastq/ that converts fasta to fastq either as standalone or unix workflow.

                      How can use I it either as standalone or unix?
                      Last edited by kaps; 05-22-2015, 12:54 AM. Reason: error posting

                      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