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  • Getting transcriptome sequence from RNA-seq reads in FASTA

    Hello,

    So, from Ensembl FTP, we can download a transcriptome file which is a FASTA file containing the header info, which is transcript name, chromosome position, etc. and the dna sequence itself. On the other hand, I have a FASTQ file from RNA-seq experiment.

    What I want to do is, generate the FASTA file like Ensembl transcriptome. I think I read this is called consensus FASTA.

    What I imagine the step to generate this is like this:

    1. Align the reads to the transcriptome reference, we get SAM/BAM
    2. Assemble the SAM/BAM according to coordinate
    3. Solve the occurence of SNP and indel
    4. Generate FASTA file with header information and sequence assembled from step 3

    For step 1, I know I can use bowtie2. For step 2, I don't know the tools but I think I can write my own program. The problem is step 3. I don't know how.
    In that case, probably you can suggest me well known pipeline to do this because I think this is a general things to do.

    What do you suggest for that? Thank you for your reply.
    Last edited by barbarian; 03-03-2016, 08:32 PM.

  • #2
    I think you can do most of what you want (following the bowtie alignment step) with samtools, using samtools sort, index, and then mpileup.

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