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bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>] |
Putting this all together and linking Let's make a link to the mirbase index directory , we have this. Go ahead and execute this from the command line – it will be fast.to make our command line simpler:
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| language | bash |
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| title | Local bowti2 alignment of miRNA data | Link to mirbase index for bowtie2 |
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cd $SCRATCH/core_ngs/align
ln -s -f $WORK/archive/referencereferences/bt2/mirbase.v20 mb20
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Putting this all together we have a command line that looks like this.
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| language | bash |
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| title | Local bowti2 alignment of miRNA data |
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bowtie2 --local -N 1 -L 16 -x mb20/hairpin_cDNA_hsa.fa -U fq/human_mirnaseq.fastq.gz -S human_mirnaseq.sam |
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- --local – local alignment mode
- -L 16 – seed length 16
- -N 1 – allow 1 mismatch in the seed
- -x mb20/hairpin_cDNA_hsa.fa – prefix path of index files
- -U fq/human_mirnaseq.fastq.gz – FASTQ file for single-end (Unpaired) alignment
- -S human_mirnaseq.sam – tells bowtie2 to report alignments in SAM format to the specified file
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Create a commands file called bt2.cmds with this task definition then generate and submit a batch job for it (time 1 hour, normal queue).
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Use nano to create the bt2.cmds file. Then: | Code Block |
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| language | bash |
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| title | Local bowti2 alignment of miRNA data |
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| launcher_creator.py -n bt2 -j bt2.cmds -t 01:00:00 -q normal
sbatch bt2.slurm; showq -u |
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When the job is complete Now you should have a human_mirnaseq.sam file that you can examine using whatever commands you like. An example alignment looks like this.
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