Sequence_2_trimmed.fq sequence_2_unpair_trimmed.fq \ Sequence_1_trimmed.fq sequence_1_unpair_trimmed.fq \ Sequence_1.fastq.gz sequence_2.fastq.gz \ YOU MUST MAKE SURE THERE IS NO SPACE AFTER THE \ Notice that since this is going to be an extremely long line, we can use a \ to tell bash interpreter that although I am not enterine a new line, do not interpret it asif I have pressed enter. Now to execute Trimmomatic let’s write out the entire line. The TRIMMOMATIC_JAR variable provides us with this path.
TRIMMOMATIC_JAR=/share/apps/trimmomatic/0.36/trimmomatic-0.36.jar TRIMMOMATIC_ROOT=/share/apps/trimmomatic/0.36 TRIMMOMATIC_HOME=/share/apps/trimmomatic/0.36 Lucky for us, once we loaded the Trimmomatic module, a new variable was placed in our environment with the path the to. Trimmomatic is a java application and for this reason, it needs to be executed with the commands java -jar followed by the actual application. Remember, to check the version number, you can simply type module avail trimmomatic In the above command, I have requested one cpu on one node for three hours and 4GB of memory. To start we must first enter the interactive session The script is useful as a reference for future use. Īlthough we have a shell script that we can simply submit using sbatch, we will perform this analysis in interactive mode. Please copy the trimming directory from our shared folderĬp -r /scratch/courses/HITS-2018/trimming.
#Geneious tutorial bam install
For convenience, IGV equates chromosome numbers and names of the form chr# (e.g., 1 and chr1 are equivalent). SAI index is an IGV format, and it does not work with samtools or any other application.Ĭhromosome names: Chromosome names must be consistent between the selected reference genome and the SAM/BAM data files. SAM files can be sorted and indexed using igvtools. The GenePattern module for sorting and indexing is Picard.SortSam. Multiple tools are available for sorting and indexing BAM files, including igvtools, the samtools package, and in GenePattern. The index files must have the same base file name and must reside in the same directory as the file that it indexes.įor example, the index file for test-xyz.bam would be named or test-xyz.bai. A SAM index filename is created by appending. Specifically, a BAM index file should be named by appending. Indexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Starting with IGV 2.0.11, IUPAC ambiguity codes in BAM files are supported. īAM, rather than SAM, is the recommended format for IGV. These formats are described on the SAM Tools web site.
A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. To load a set of BAM files merged into a single track see Merged BAM File.Ī BAM file (.bam) is the binary version of a SAM file.
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