Extracting transcripts from whole-transcriptome libraries

Question

[julianneradford]

Hi there,

I am having trouble finding a tool that will successfully extract specific transcripts from whole transcriptome libraries. The transcriptome libraries were assembled through Trinity, and the reference transcriptome was a de novo assembly from Trinity also.

My ultimate goal is to extract the transcripts of interest, and then compare SNP counts and calculate dN/dS ratios. Any help is appreciated. Thanks.

[GenoMax]

extract specific transcripts from whole transcriptome libraries

Define specific. Particular proteins/genes? In any case you will have to identify a reference set by annotating one library and then you can identify transcripts of interest from others by sequence searching.

[julianneradford]

By specific I mean genes, yes. I have 9 fastq transcriptome libraries that have been mapped to an annotated reference transcriptome, and I generated VCFs as well. I would like to pull the same specific genes (each sequence ("gene") is labelled with it's trinity identifier) from each of the fast q libraries. Do you know of a tool that sequence searches and pulls out specific sequences from either BAM or VCF files?