Dear all,
i am trying to run TopHat on the RNA-seq datasets from Chris Burge's Lab (published in Nature 2008). However, TopHat seems to require gigantic amounts of disk space for its tmp file left_kept_reads.fq.candidate_hits.sam .
Just using 500.000 RNA-seq reads from the liver library (32bp long single end reads) it generated a 82GB left_kept_reads.fq.candidate_hits.sam file. Final output looks reasonable though.
Any ideas where the problem might lie ... or is that normal?
Many thanks for your help!!
Heather
i am trying to run TopHat on the RNA-seq datasets from Chris Burge's Lab (published in Nature 2008). However, TopHat seems to require gigantic amounts of disk space for its tmp file left_kept_reads.fq.candidate_hits.sam .
Just using 500.000 RNA-seq reads from the liver library (32bp long single end reads) it generated a 82GB left_kept_reads.fq.candidate_hits.sam file. Final output looks reasonable though.
Any ideas where the problem might lie ... or is that normal?
Many thanks for your help!!
Heather
Comment