alignment used for CCLE RNA-seq

Question

[Amos]

Hi.

I recently downloaded the CCLE RNA-seq bam files from the GDC legacy archive. I'm trying to figure out which program was used to align the reads but can't find the documentation for the RNA-seq protocol. Does anyone know how the reads were aligned? I tried emailing the CCLE help but haven't gotten a reply.

Thank you.

Answer 1

[dyollluap]

It's in the associated analysis metadata files:

<pipe_section> <step_index>tophat</step_index> <prev_step_index>N/A</prev_step_index> <program>tophat</program> <version>v1.4.1</version> <notes>tophat.sh -o tophat_out --num-threads $NSLOTS --mate-inner-dist 300 --mate-std-dev 500 --no-sort-bam --no-convert-bam --GTF Homo_sapiens_assembly19.gtf --transcriptome-index annotation Homo_sapiens_assembly19 1.fastq .2.fastq</notes> </pipe_section>