Changes between Version 3 and Version 4 of SOPs/AssemblingRNAseqReads


Ignore:
Timestamp:
04/27/17 08:39:58 (8 years ago)
Author:
gbell
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/AssemblingRNAseqReads

    v3 v4  
    11== De novo assembly of short reads with inchworm ==
    2 * [http://trinityrnaseq.sourceforge.net/ Inchworm RNA-Seq Assembler] - official project page
     2* [https://github.com/trinityrnaseq/trinityrnaseq/wiki Inchworm RNA-Seq Assembler] - official project page for Trinity, of which it is one part
    33* It can require large amounts of memory (with large datasets), limiting the size of the set of reads that can be assembled at once.
    44* Based on planarian 36-nt reads, this appears to work better than velvet or tophat+cufflinks.
    … …  
    2020== Discovering novel genes and transcripts with tophat and cufflinks ==
    2121
    22 Reference: [http://tophat.cbcb.umd.edu/ tophat] [http://cufflinks.cbcb.umd.edu/tutorial.html cufflinks]
     22Reference: [http://ccb.jhu.edu/software/tophat/index.shtml tophat] [http://cole-trapnell-lab.github.io/cufflinks/ cufflinks]
    2323
    2424The 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.
    … …  
    26261. Map the reads for each sample to the reference genome.  Output from TopHat (accepted_hits.bam) can be used as input for cufflinks.
    2727
    28   See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
     28  See our [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
    2929
    30302. Run Cufflinks on each mapping file: use -M to ignore all reads mapped to rRNA and mitochondrial transcripts, this will increase speed and performance.
    … …  
    5959
    6060* [http://www.broadinstitute.org/software/scripture/ Scripture]
    61 * [http://www.broadinstitute.org/scientific-community/software/trinity Trinity] - includes inchworm together with other methods
    62 See the [http://www.the-dream-project.org/result/alternative-splicing DREAM “alternative splicing”] challenge for bake-off description and results
     61* [https://github.com/trinityrnaseq/trinityrnaseq/wiki Trinity] - includes inchworm together with other methods
     62See the [https://www.synapse.org/Portal.html#!Synapse:syn2817724/wiki/70952 DREAM Alternative Splicing Challenge] for bake-off description and results
    6363
    6464