Results for "Master"

Bio-Scripts

  • Estimate Genome Size

    # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19

    2217 days ago

  • Mapping with BWA-mem or BWA-sampe in one go with python script !

    ...ad mode. BESST provides a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py)...aired read alignment pipeline. https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py

    2077 days ago

  • BloomFilter

    ➜ Tools git:(master) ✗ git clone git://github.com...ivity... done. ➜ Tools git:(master) ✗ cd bloomfilter ➜ bloomfilter git:(master) ls AUTHORS COPYING...mfilter' ➜ bloomfilter git:(master) ✗ pwd /home/urbe/Tools/bloo...mfilter' ➜ bloomfilter git:(master) ✗ pwd /home/urbe/Tools/bl...

    2104 days ago

  • Running Trinity on RNA-seq !

    ➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType fq --max_memory 250G --left /media/urbe/MyPassport/rnaseq_boris/AIG_AAAOSW_8_1_C1CBGACXX.IND11_noribo_clean.fastq --...

    2080 days ago

  • Fastq-dump for SRA download

    ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...] ./fastq-dump [options] INPUT -A|--accession Replaces accession derived f...

    2079 days ago

  • Installing Porechop on Ubuntu !

    ➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Po...king connectivity... done. ➜ Tools git:(master) ✗ cd Porechop ➜ Porechop git:(master) python3 setup.py install ru...home/urbe/anaconda3/bin ➜ Porechop git:(master) porechop -h usage: porechop...

    2059 days ago

  • Installing NextSV on Ubuntu !

    ➜ Tools git:(master) ✗ git clone https://github.c...ivity... done. ➜ Tools git:(master) ✗ cd nextsv ➜ nextsv git:(master) pip install argparse Collec...ervalTree-0.5 ➜ nextsv git:(master) sh install_pbhoney.sh ####...fles finished ➜ nextsv git:(master) ✗

    2052 days ago

  • Downloading GATK !

    ...LOCAL: run using the in-memory spark runner SPARK: run using spark-submit on an existing cluster --spark-master must be specified...

    2028 days ago

  • Update zsh on Ubuntu !

    .../github.com/robbyrussell/oh-my-zsh * branch master -> FETCH_HEAD 9544316e..dc8811f8 master -> origin/master Updatin...100644 => 100755 themes/trapd00r.zsh-theme Current branch master is up to date. __...

    2027 days ago

  • Installing nupack3.0.6

    #http://www.nupack.org/downloads/source ➜ tools git:(master) ✗ cd nupack3.0.6 ➜ nupack3.0.6 git:(master) ✗ make make -C src/ make[1]: Entering directory '/home/urbe/Tools/nupack3.0.6/nupack3.0.6/src'...

    1979 days ago