This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RNA-Seq raw fastq files from TCGA

Dear group,

I am looking for raw FASTQ files for RNA-Seq TCGA data. The BAM files were made using reads that map only to known genes. I am looking to get FASTQ files that were not filtered in anyway to retain reads mapping to known genes only.

I have access to Level 1 data through an approved protocol.

Thanks Adrian.

rna-seq tcga fastq
• 9,191 views • link
written by oriolebaltimore oriolebaltimore

Sorry - I forgot to add that - is it possible to get raw FASTQ files from TCGA. Thanks

• 0 views • link
written by oriolebaltimore oriolebaltimore

Are you sure about that? You can see the command line used to map the reads in the BAM header. Nowhere do I see anything that suggests that only reads mapping to known genes were kept? Only known genes were used when quantifying, but that's different.

Fastq's only exist in the TCGA legacy archive, whic hI don'tthink contains everything.

• 0 views • link
written by i.sudbery i.sudbery

that's correct. you just need to convert the supplied bam files to raw reads available through GDC.

here's an pipeline example: https://github.com/mforde84/TCGA-BRCA-RNAseq-realignment-pipeline

also from experience, converting bam to fastq is a bottleneck. picard has an option but it's really slow. the scripting provided above has a custom solution called fasty to do this. however i couldn't locate my source code. instead you could use something like the following which should be as fast: https://github.com/arq5x/bedtools2/blob/master/src/bamToFastq/bamToFastq.cpp

• 0 views • link
written by mforde84 mforde84

0 answers

No answers yet.

Log in to answer this question.

More posts like this