Hi, Recently I have checked the length distribution of RNA-seq reads in BAM files with Fastqc tool. It turns out that the length of all reads is 101bp. Can someone explain why there is just one kind of length? Can Illumina Hiseq 2000/2500 sequencers just output specified length reads, or reads with other lengths were removed before uploading to Synapse? Thanks.

Created by Rui Chang, Ph.D. ruichang
Thanks! You'll get a faster response if you ask in the AMP-AD discussion forum. You can post your question here: https://www.synapse.org/#!Synapse:syn2580853/discussion/
I am asking questions about data in AMP-AD project. Rui
@xujishu Thanks, I already got the information I want.
I am not sure I understand you question, Illumna only produce 101bp sequencing reads for this experiment.
@xujishu Thanks for your reply. In the Mayo RNAseq dataset of AMP-AD (https://www.synapse.org/#!Synapse:syn3163039), as the experiment design said, Illumina HiSeq 2000 sequencers were used for 101 base pair (bp) paired-end sequencing with triplicate multiplexing of barcoded samples (3 samples per flowcell lane). The results of fastqc tool also validated the length of reads only contains 101 bp. My question is why the shorter reads have not stored in the bam files if the sequencing window is 101 bp. Thanks.
Hi Rui Chang, Besides 101bp read length, there could be 25bp, 50bp, 75bp or 150bp. There is no 'standard' read length for RNA-Seq sequencing production. For one type sequencer, such as HiSeq2500, the total capacity(total bases can be sequenced) is fixed, so you either can sequence more reads but with short read length, or sequence longer reads but at low coverage(less reads). So at the end, the read length is really depended on your experiment design and budge. -Jishu
Hello, which project are you referring to? Posting into the discussion forum on that project will assure someone with the knowledge will be able to help. Thanks!

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