Hi There, Just a quick question on reads mapping problem in ROSMAP RNA-seq part( syn3388564 ). It says "We used the non-gapped aligner Bowtie to align reads to transcriptome reference and then applied RSEM to estimate expression levels for all transcripts. The FPKM values were the outcome of our data RNA-Seq pipeline. " I want to know if reads are uniquely mapped or not, when you measure FPKMs. Is the RNA-seq pipeline available on github or somewhere else? Thanks! Best, Tao

Created by Tao Wang twang
Thanks Ben and Jishu! Hi Jishu, I'd like to know more details about how the RNA-seq bam files were generated. Reads were aligned onto genome reference OR transcriptome reference? Using bowtie? I feel a little lost on the processing pipeline. Would you please help me clarify the pipeline generally(from raw reads to bam files then to RPKMs)? Thanks for your help! Best, Tao
I would say NO. When we ran Trinity (Bowtie1 as aligner) and RSEM, we did not specified any parameters to deal with "un-unique mapping" reads.
Hi Tao, I'll defer to @xujishu to answer your question concerning their version of the ROSMAP RNAseq data. We also will be releasing a reprocessed version of the ROSMAP RNAseq data later this summer with the full pipeline. Best, Ben

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