Results for "master in bioinformatics"
Bio-Scripts
# 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 dataframe192258 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read...s a script (https://github.com/ksahlin/BESST/blob/master/scripts/reads_to_ctg_map.py)...ipeline. https://github.com/ksahlin/BESST/blob/master/scripts...2118 days ago
- ...ivity... done. ➜ Tools git:(master) ✗ cd bloomfilter ➜ bloomfilter git:(master) ls AUTHORS COPYING...e --init ➜ bloomfilter git:(master) ./autogen.sh + aclocal + a...mfilter' ➜ bloomfilter git:(master) ✗ pwd /home/urbe/Tools/bloo...mfilter' ➜ bloomfilter git:(master) ✗ pwd...
2145 days ago
- ➜ 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....
2121 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...] ./fastq-dump [options] INPUT -A|--accession Replaces accession derived...
2120 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git Cloni...cking connectivity... done. ➜ Tools git:(master) ✗ cd Porechop ➜ Porechop git:(master) python3 setup.py install ru.../home/urbe/anaconda3/bin ➜ Porechop git:(master) porech...2100 days ago
- ...ivity... done. ➜ Tools git:(master) ✗ cd nextsv ➜ nextsv git:(master) pip install argparse Collec...ages (0.14.1) ➜ nextsv git:(master) pip install networkx Requir...ervalTree-0.5 ➜ nextsv git:(master) sh install_pbhoney.sh ####...fles finished ➜ nextsv git:(master) ✗
2092 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-...run using spark-submit on an existing cluster --spark-master must be...
2069 days ago
- ➜ upgrade_oh_my_zsh Updating Oh My Zsh remote: Counting objects: 484, done....russell/oh-my-zsh * branch master -> FETCH_HEAD 9544316e..dc8811f8 master -> origin/master Updatin...themes/trapd00r.zsh-theme Current branch master is up t...
2068 days ago
- #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'...
2020 days ago
