Name: Host-Screen
Owner: Hurwitz Lab
Description: Utilizes Bowtie2 to remove host contaminated read from Fasta/q files
Created: 2016-11-02 18:59:37.0
Updated: 2016-11-02 20:57:06.0
Pushed: 2016-12-19 17:22:18.0
Homepage: null
Size: 4
Language: Shell
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Utilizes Bowtie2 to remove host contaminated read from Fasta/q files
Before Start:
A Bowtie2 index must be created prior to using this program. The index should be created from the genome(s) of what your screening for (i.e. to remove human reads a index from the human genome needs to be created). The index is created from fasta/q files from the host using bowtie2-build:
bowtie2-build [options]*
$ bowtie2-build chr1.fa,chr2.fa,chrX.fa,chrY.fa human_index -f
(human_index is the bt2_base and is used as the INDEX_BASE variable in settings.sh)
(-f signifies the reference input files are in FASTA format)
Instructions:
1) Edit settings.sh to include correct paths (See below for variable descriptions)
2) Move into the directory containing your FASTA/Q files. Create a file named “list” that contains the BASENAME of your paired end files. An example of this process is demonstrated below:
$ cd fasta/
$ ls *.fasta > list
$ sed -i -e 's/.fasta//g' list
$ cat list
SRR1647144
SRR1647145
SRR1647236
SRR1647237
SRR1647238
SRR1647239
SRR1647240
SRR1647260
3) Edit the “naming scheme” in host-screen.sh (found in script directory). The naming scheme declares the extensions to differentiate between forward/reverse/singleton paired end files.
4) Execute submit.sh
$ ./submit.sh
Variable Descriptions:
These are descriptions of the variables found in settings.sh that must be edited before submitting the job.
FASTA_DIR=“/path/to/fasta(or fastq)/files”
FORMAT=“f” or “q” (f = fasta format, q = fastq format)
INDEX_DIR=“/path/to/bt2/index”
INDEX_BASE=“basename” of the Bowtie 2 index files as named during bowtie2-build
OUT_DIR=“/path/to/store/screened/reads”
THREADS=“number cpus”