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Old 03-03-2012, 05:52 AM   #1
Location: Italy

Join Date: Mar 2012
Posts: 10
Default Extracting full length mRNA sequencens from BAM file

Hi everyone,
this is my first post so, please be patient!
I'm trying to create a blast DB using the RNAseq data from ENCODE.
I've downloaded both the FASTQ reads and the .bam/bai files.
Is it possible to extract the fasta sequences of all the transcript from the BAM file?
Alternatively should i try to do a de novo assembly using Trinity?
Thanx a lot.

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