How to get a contig of the transcripts for genes from mapped file?

[super0925]

How to get a contig of the transcripts for genes from mapped file?
I want output a sequence as a result of generating a contig from the mapped sequence data. Thank you!

[GenoMax]

Take a look at this thread: http://seqanswers.com/forums/showthread.php?t=28281

I assume you know the boundaries of your genes so you could use the -r (region) option with samtools mpileup to get consensus sequence. Keep in mind that this is not going to give you sequences for alternate transcripts (if there are any in that region).

[super0925]

Take a look at this thread: http://seqanswers.com/forums/showthread.php?t=28281

I assume you know the boundaries of your genes so you could use the -r (region) option with samtools mpileup to get consensus sequence. Keep in mind that this is not going to give you sequences for alternate transcripts (if there are any in that region).

Thanks.

(1)Do you mean this command:

samtools mpileup -uf [B][I]reference_genome.fa aligned.bam[/I][/B] | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

(2)
And if I use -r option, how do I define the gene's start and end

for example, this is the gene annotaion file GTF file

chr1    unknown exon    11874   12227   .       +       .       gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018"; tss_id "TSS14844";
chr1    unknown exon    12613   12721   .       +       .       gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018"; tss_id "TSS14844";
chr1    unknown exon    13221   14409   .       +       .       gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018"; tss_id "TSS14844";

for gene DDX11L1, is the location the -r ch01: 11874-14409? I am sorry to ask this naive question.

[GenoMax]

That should cover the region for those three exons.