Hi everyone,
I'm using TopHat to map my RNA-seq reads to splice junctions for use in Cufflinks, but it's been taking a bit longer than I expected. One sample I ran (as an initial test) has been going for ~34 hours, and the tophat_out folder is using up around 76 GB of space. By looking in the logs, it seems to be on the "segment_juncs" step.
Each of the individual samples I hope to align have roughly 90 million reads (@ 50 nt) over 3 lanes, and I'm aligning to the human genome (hg19).
Would anyone know how long I should expect the program to run for, and also how much disk space it'll need per sample?
Thanks!
edit: I'm using single-end reads
I'm using TopHat to map my RNA-seq reads to splice junctions for use in Cufflinks, but it's been taking a bit longer than I expected. One sample I ran (as an initial test) has been going for ~34 hours, and the tophat_out folder is using up around 76 GB of space. By looking in the logs, it seems to be on the "segment_juncs" step.
Each of the individual samples I hope to align have roughly 90 million reads (@ 50 nt) over 3 lanes, and I'm aligning to the human genome (hg19).
Would anyone know how long I should expect the program to run for, and also how much disk space it'll need per sample?
Thanks!
edit: I'm using single-end reads
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