newbie

I am want to do some RNA seq differential expression experiments using our lab-specific reference index. I need FASTQ files. I know the raw reads including unmapped reads are available in the BAM files. (https://www.gtexportal.org/home/faq#obtainFastq)

Do I need to trim the reads? I could not find any information about adaptors, or if the GTEx BAM/FASTQ files are trimmed or not

I looked through the GTEx TOPMed pipeline for hints. I did not find a 'trim" task

I appreciate any suggestions.

Andy

https://github.com/broadinstitute/gtex-pipeline https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq

GTEx RNASeq pipe https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/rnaseq_pipeline_bam.wdl

https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/samtofastq.wdl

https://github.com/broadinstitute/gtex-pipeline/blob/master/rnaseq/star.wdl