Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Eland export to sam

    Hello all,

    After converting Eland alignment export files to sam, I tried to convert sam to bam by samtools view -bt ref.fa.fai,

    what do these mean shown on the screen? Thanks.

    [sam_read1] reference 'chr11.fa' is recognized as '*'.
    [sam_read1] reference 'chr6.fa' is recognized as '*'.
    [sam_read1] reference 'chr6.fa' is recognized as '*'.
    [sam_read1] reference 'chr11.fa' is recognized as '*'.
    [sam_read1] reference 'chr11.fa' is recognized as '*'.
    [sam_read1] reference 'chrY.fa' is recognized as '*'.
    [sam_read1] reference 'chr1.fa' is recognized as '*'.
    [sam_read1] reference 'chr1.fa' is recognized as '*'.
    [sam_read1] reference 'chrX.fa' is recognized as '*'.

  • #2
    @bair,
    Did you find a solution for this problem?

    Comment


    • #3
      Nevermind... The ELAND alignment from our Core used a 'chrN.fa' reference, whereas the hg19.fa uses just 'chrN'. Adding a --nofa tag to export2sam.pl with "if($nofa > 0){$t[EXPORT_CHROM] =~ s/.fa//g};" got us back on track.

      Comment


      • #4
        Originally posted by pharmbot View Post
        Nevermind... The ELAND alignment from our Core used a 'chrN.fa' reference, whereas the hg19.fa uses just 'chrN'. Adding a --nofa tag to export2sam.pl with "if($nofa > 0){$t[EXPORT_CHROM] =~ s/.fa//g};" got us back on track.
        OR, you could just do a sed s/.fa// on the input file before doing export2sam.pl

        Comment


        • #5
          How did you convert the ELAND alignment ouput file to sam? I have scoured the web/literature and cannot find out how to do this.

          Comment


          • #6
            Originally posted by kreitinger View Post
            How did you convert the ELAND alignment ouput file to sam? I have scoured the web/literature and cannot find out how to do this.
            One way to do this is using Illumina's casava software's helper script illumina2sam.pl

            Comment


            • #7
              Thanks, I will look into that. One problem, though, is I do not have access to the Illumina software and was hoping there was some opensource software instead.

              Comment


              • #8
                there is a script export2sam.pl in samtools package (opensource) that may help you.

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  The Impact of AI in Genomic Medicine
                  by seqadmin



                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                  02-26-2024, 02:07 PM
                • seqadmin
                  Multiomics Techniques Advancing Disease Research
                  by seqadmin


                  New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

                  A major leap in the field has
                  ...
                  02-08-2024, 06:33 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Yesterday, 06:12 AM
                0 responses
                17 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-23-2024, 04:11 PM
                0 responses
                67 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-21-2024, 08:52 AM
                0 responses
                73 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-20-2024, 08:57 AM
                0 responses
                62 views
                0 likes
                Last Post seqadmin  
                Working...
                X