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  • dena.dinesh
    Member
    • Feb 2013
    • 58
    #1

    extracting complete sequence for every transcript from a bam file

    hi,

    I have bam obtained by aligning to a transcriptome. Is it possible to obtain the complete sequence that has been aligned to every transcript and make a fast file out aligned sequences for every transcript. For an example, if the complete aligned sequence with respect to reference trasncript is like
    Code:
    >ref_tr1
aggtcgtttagtcgatatcgtga
>aln_tr1
a-gtcgtttagtcgat-tcgtga
    I would like to obtain a fasta file containing only aligned trasncripts like
    Code:
    >aln_tr1
a-gtcgtttagtcgat-tcgtga
>aln_tr2
agtgtcgggctgag--gcg-cc
    How can I obtain this fast file from aligned bam file. Kindly guide me.
    Thanks in advance
    Last edited by dena.dinesh; 08-04-2015, 02:27 AM.
    Tags: bam, rnaseq, samtools
  • rnaeye
    Member
    • May 2011
    • 80
    #2
    Of course it's possible. You can use "bedtools."

    Comment

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