Easiest Way to Download All Sra Samples or Multi Experiment file from NCBI SRA database- II

Previously I shared a easy way to download the data files from NCBI SRA database. Although it took only wget to download the data files but it required lots of link editing. Here I am going to share another script which can download all files of any biostudy or a single file, depending upon the accession number provided to the script. This bash script will also simultaneously convert the native sra file into fastq files also. Hope it will be some help.


if [ "$#" -eq  "0" ]
   echo "No accession number provided"
   exit 1
   echo -n "Please wait...."
   esearch -db sra -query $id  | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | xargs fastq-dump --split-files
   echo -n "Download complete...."

Save the script as sra_download.sh and run as
 bash sra_download.sh SRA_accession_number 
You can use any kind of accession number including SRR3114162, PRJNA309373 or SRP068795. I have tested this script on Ubuntu and assume that Entrez Direct and NCBI SRA Toolkit is installed on your machine.
Extract Part of a FASTA Sequences with Position by python script HERE

How To Predict CRISPR-Cas9 target site in R

Although there are several online bioinformatics tools to predict the target site for CRISPR-Cas9 but I was looking for a offline solution. I am going to share a R script that use two R libraies CRISPRseek and msa. The best part is that it also predict the restriction enzyme sites in target region therefore it will help in downstream analysis of mutant screening. Hope this script will help some one. As always R script is heavily commented to get it easy.

How To Perform Basic Multiple Sequence Alignments In R HERE

Journal Citation Reports 2015 / 2016