Filter a CASAVA-generated fastq file¶
Note
Required OS: | OS x or Linux. Windows users, please contact Saranga Wijeratne |
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Software: | Illumina CASAVA-1.8 FASTQ Filter |
Purpose: | This document provides instructions about how to remove Passing Filter (PF) failed reads from a Fastq file |
More: | Read more about PF here: and here |
Author: | This document was created by Saranga Wijeratne |
Software installation¶
Note
If you are runing this on MCBL mcic-ender-svr, please skip the installation. Following command will load the software module to your environment.
1 | $ module load fasq_filter/0.1
|
On your own server,
Warning
If you don’t have administrator privileges on the machine, you wouldn’t be able run sudo
(last command in the following code block) commands.
1 2 3 4 5 | $ wget http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/fastq_illumina_filter-0.1.tar.gz
$ tar -xzf fastq_illumina_filter-0.1.tar.gz
$ cd fastq_illumina_filter-0.1
$ make
$ sudo cp fastq_illumina_filter /usr/local/bin
|
Tip
Put your executables in ~/bin
or full-path to executables in $PATH
in the absence of sudo
privilages.
Filter a fastq file¶
Input File: | C8EC8ANXX_s2_1_illumina12index_1_SL143785.fastq.gz |
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Output File: | C8EC8ANXX_s2_1_illumina12index_1_SL143785.filtered.fastq.gz |
1 | $ zcat C8EC8ANXX_s2_1_illumina12index_1_SL143785.fastq.gz | fastq_illumina_filter -vvN | gzip > C8EC8ANXX_s2_1_illumina12index_1_SL143785.filtered.fastq.gz
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Filter multiple fastq files¶
Input File: | Fastq_filenames.txt |
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Output Files: | Individual Fastq files |
Create a Fastq_filenames.txt file with your Fastq filenames in seperate lines as follows:
#Content of Samples.txt C6V7FANXX_s8_0_TruseqHTDual_D712-TruseqHTDual_D508_SL104628.fastq.gz C6V7FANXX_s3_0_TruseqHTDual_D703-TruseqHTDual_D501_SL104549.fastq.gz C6V7FANXX_s5_0_TruseqHTDual_D709-TruseqHTDual_D506_SL104602.fastq.gz C6V7FANXX_s8_0_TruseqHTDual_D705-TruseqHTDual_D501_SL104565.fastq.gz
Save the above file in the same folder with your Fastq files.
Use the Terminal and navigate to the location where Fastq_filenames.txt is saved.
1 2
#If your Fastq_filenames.txt is saved under ~/Downloads $ cd ~/Downloads
Type in the following command to filter Fastqs in the Fastq_filenames.txt.
1
$ for f in $(cat Fastq_filenames.txt); do zcat $f | fastq_illumina_filter -vvN | gzip > ${f%.*.fastq.gz}.filtered.fastq.gz;done