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Use our summer school reservation (CoreNGS-Wed) when submitting batch jobs to get higher priority on the ls6 normal queue today.
Note that the reservation name (CoreNGS-Wed) is different from the TACC allocation/project for this class, which is OTH21164. |
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# Load the main BioContainers module then load the fastqc module module load biocontainers # make take a while module load fastqc |
It has a number of options (see fastqc --help | more) but can be run very simply with just a FASTQ file as its argument.
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Make sure you're in an idev session. If you're in an idev session, the hostname command will display a name like c455-021.ls6.tacc.utexas.edu. But if you're on a login node the hostname will be something like login3.ls6.tacc.utexas.edu. If you're on a login node, start an idev session like this:
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FASTX Toolkit is available as a BioContainers module.
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Because the [-i INFILE] [-o OUTFILE] options are shown in brackets [ ], reading from a file and writing to a file are optional. That means that by default the program reads its input data from standard input and writes trimmed sequences to standard output:
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- The -l 50 option says that base 50 should be the last base (i.e., trim down to 50 bases)
- The -Q 33 option specifies how base Qualities on the 4th line of each FASTQ entry are encoded.
- TheĀ FASTX Toolkit is an older program written in the time when Illumina base qualities were encoded differently, so its default does not work for modern FASTQ files.
- These days Illumina base qualities follow the Sanger FASTQ standard (Phred score + 33 to make an ASCII character).
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Make sure you're in an idev session. If you're in an idev session, the hostname command will display a name like c455-021.ls6.tacc.utexas.edu. But if you're on a login node the hostname will be something like login3.ls6.tacc.utexas.edu. If you're on a login node, start an idev session like this:
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module load biocontainers
module spider cutadapt
module load cutadapt
cutadapt --help | more
cutadapt --help | less |
A common application of cutadapt is to remove adapter contamination from RNA library sequence data. Here we'll show that for someĀ small RNA libraries sequenced by GSAF, using their documented small RNA library adapters.
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Read more about Arithemetic in bash and more about awk in Some Linux commands: awk |
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Looking at the FASTQ file names, we see this is two lanes of single-end reads (L004 and L005). The data from lane 4 has 2,001,337 reads, the data from lane 5 has 2,022,237 reads. |
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