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  • tophat strand info?

    can anyone help me identify if the strand info is in the accepted.sam file (tophat output)
    SOLEXA1_0001:1:60:7595:15462#0 16 chr1 3000555 255 36M * 0 0 AATTTGTTTTGTCCTTCAGCGGATTAAAATATTCAG CBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0

    or does anyone know what is column 2 and 4 means. I checked sam manual but still confused. Thanks.

  • #2
    Hi,

    The strand info will only be on the junction reads. It is impossible to determine the strand of non-junction hits without using a stranded protocol in the experiment.

    column 2 is the SAM flag. You can google "SAM flag" to find out.

    column 4 is the chromosome start location of the hit.
    SpliceMap: De novo detection of splice junctions from RNA-seq
    Download SpliceMap Comment here

    Comment


    • #3
      Hey,

      I just came accross the same problem and found that you can read strand info from the
      2nd colunmn. This is actually a flag that has to be deciphered according to the SAM format and can be done for instance here:

      In your case, 16 means that this read is on the reverse strand.
      Column 4 is the start postition of this read on the respective chromosome.
      Note, since tophat produce BAM formats as default for a while, you can still
      access the flag information with:
      samtools view accepted_hits.bam
      which produces SAM format.

      cheers
      Sebastian

      Comment

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