Changes between Version 5 and Version 6 of SOPs/AssemblingRNAseqReads


Ignore:
Timestamp:
09/21/20 16:35:41 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/AssemblingRNAseqReads

    v5 v6  
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    67 == Cluster sequences with TGICL ==
     67== Clustering sequences with TGICL ==
    6868
    69 
    70 {{{
    71   TGICL was designed for the assembly of longer transcript fragments like ESTs. 
    72   It can still be useful for the multi-step assembly of large or heterogeneous transcript fragments. 
    73   In these cases, short read assemblers can be used as a first step to generate longer contigs (of variable lengths) which can be further assembled with TGICL.
    74 }}}
     69TGICL was designed for the assembly of longer transcript fragments like ESTs. 
     70It can still be useful for the multi-step assembly of large or heterogeneous transcript fragments. 
     71In these cases, short read assemblers can be used as a first step to generate longer contigs (of variable lengths) which can be further assembled with TGICL.
    7572
    7673{{{
    … …  
    8178== Cleaning the assembled sequence ==
    8279
     80Short reads should be generally cleaned of vector/linker/primer sequences before assembly.
     81In some cases we may have pre-assembled contigs that can still contain contamination.
    8382
    8483{{{
    85   Short reads should be generally cleaned of vector/linker/primer sequences before assembly.
    86   In some cases we may be pre-assembled contigs that can still contain contamination.
    87  
    88   Sample command: In this example, contig.fa is the output file from above assembly step
    89   bsub "seqclean contig.fa -v /nfs/genomes/UniVec/UniVec_Core -o contig_cleaned.fa"
     84# Sample command: In this example, contig.fa is the output file from above assembly step
     85bsub "seqclean contig.fa -v /nfs/genomes/UniVec/UniVec_Core -o contig_cleaned.fa"
    9086}}}
    9187