Changes between Version 2 and Version 3 of SOPs/AssemblingRNAseqReads
- Timestamp:
- 09/11/13 15:00:39 (11 years ago)
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SOPs/AssemblingRNAseqReads
v2 v3 24 24 The de novo assembly worked fine in 100bp pair-end reads. For the six 40bp pair-ends reads samples in our hands, cufflinks failed at creating decent amount of junctions. For short reads (usually <45-bp), it is better to decrease segment length (–segment-length) to about half the read length and segment mismatches (–segment-mismatches) to 0 or 1. 25 25 26 1. Map the reads for each sample to the reference genome : accepted_hits.bam from tophat can be used as input for cufflinks26 1. Map the reads for each sample to the reference genome. Output from TopHat (accepted_hits.bam) can be used as input for cufflinks. 27 27 28 28 See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
