Page Comparison

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idev -m 120 -A OTH21164 -N 1 -r CoreNGS-Thu      # or -A TRA23004 
# or
idev -m 90 -A OTH21164 -N 1 -p development   # or -A TRA23004 

Go ahead and load the bowtie2 module so we can examine some help pages and options.

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idev -m 120 -A OTH21164  -N 1 -r CoreNGS-Thu    # or -A TRA23004
# or
idev -m 90 -A OTH21164 -N 1 -p development  # or -A TRA23004

module load biocontainers
module load bowtie2

...

module load samtools
cd $SCRATCH/core_ngs/alignment/vibCho
bowtie2 --local -x vibCho/vibCho.O395 -U fq/cholera_rnaseq.fastq.gz 2>aln_local.log | \
 | samtools view -b > cholera_rnaseq.local.bam

89006 reads; of these:
  89006 (100.00%) were unpaired; of these:
    13359 (15.01%) aligned 0 times
    46173 (51.88%) aligned exactly 1 time
    29474 (33.11%) aligned >1 times
84.99% overall alignment rate

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Using bwa mem for RNA-seq alignment is sort of a "poor man's" RNA-seq alignment method. Real splice-aware aligners like tophat2STAR, hisat2 or STAR tophat have more complex algorithms (as shown below) – and take a lot more time!

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BWA MEM does not know about the exon structure of the genome. But it can align different sub-sections of a read to two different locations, producing two alignment records from one input read (one . One of the two will be marked as secondary (0x100 flag).

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# Make sure you're in an idev session
idev -m 120 -N 1 -A OTH21164 -r CoreNGS-Thu      # or -A TRA23004
# or
idev -m 90 -N 1 -A OTH21164 -p development   # or -A TRA23004

# Load the modules we'll need
module load biocontainers
module load bwa
module load samtools

# Copy over the FASTQ data if needed
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*.gz $SCRATCH/core_ngs/alignment/fastq/

# Make a new alignment directory for running these scripts
cds
mkdir -p core_ngs/alignment/bwamem
cd core_ngs/alignment/bwamem
ln -sf ../fastq
ln -sf /work/projects/BioITeam/ref_genome/bwa/bwtsw/hg38

Now take a look at bwa mem usage (type bwa mem with no arguments, or bwa mem 2>&1 | more). The most important parameters are the following:

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cd $SCRATCH/core_ngs/alignment/bwamem
bwa mem -M hg38/hg38.fa fastq/human_rnaseq.fastq.gz 2>hs_rna.bwamem.log | \
  samtools view -b | \
  samtools sort -O BAM -T human_rnaseq.tmp > human_rnaseq.sort.bam

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