Question: Questions about MaSuRCA assembly program
1
gravatar for arnstrm
4.6 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:

Hi all,

I have few questions about MaSuRCA assembly program and I will greatly appreciate if anyone can clarify these doubts:

  1. Do I have to run trimmomatic or any other filtering/trimming tools before I run the assembly? I am asking this because the program already has a inbuilt error correction step.
  2. How to specify the overlapping libraries ? The sr-config file asks to provide input library as 1)two_letter_prefix 2)mean 3)stdev 4)fastq 1 5) fastq 2, but negative mean are to specify paired-end reads that are outies (RF) and it won't accept 0 as insert size. Also, is the mean, insert-size or the total size (read length * 2 + insert size)?
  3. Do I have to combine similar library types into a single file before putting them in sr-config file or is it OK to specify each library separately?

Thanks very much,

ADD COMMENTlink modified 4.6 years ago by rtliu2.0k • written 4.6 years ago by arnstrm1.7k
4
gravatar for rtliu
4.6 years ago by
rtliu2.0k
New Zealand
rtliu2.0k wrote:

1. No need to run trimmomatic. the inbuilt error correction step has adapter trimming, error correction, etc.

2. Read the quick start guide (ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf).  e.g.

   PE = aa 180 20 /data/fwd_reads.fastq /data/rev_reads.fastq
   The 'mean' and 'stdev' parameters are the library insert average length and standard deviation. 

   "JUMP are assumed to be outties <---.--->. If there are any jump libraries that are innies, such as longjump,

    specify them as JUMP and specify NEGATIVE mean."  So negative mean is for longjump library, not

     for paired-end reads.

3. No, you can specify each library per line, e.g. add a new line, supposed 250bp PE library with 30bp stdev

    PE = bb 250 30 /data/fwd_reads_1.fastq /data/rev_reads_1.fastq

Good luck!

 

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by rtliu2.0k

Thanks very much for answering! I am still not getting the second question. If I have overlapping libraries (miseq) of length 250bp (R1=250bp, R2=250bp), with 50bp overlap, what would be the insert size? will it be the total length (450bp) or insert size (-50bp)?

Thanks once again!

 

ADD REPLYlink written 4.6 years ago by arnstrm1.7k
1

insert size = 450bp

ADD REPLYlink written 4.6 years ago by rtliu2.0k
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