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Since the BAM file contains records for both mapped and unmapped reads, just counting records doesn't provide information about the mapping rate of our alignment. The samtools flagstat tool provides a simple analysis of mapping rate based on the the SAM flag fields.

Here's how to run samtools flagstat and both see the output in the terminal and save it in a file – the samtools flagstat standard output is piped to tee, which both writes it to the specified file and sends it to its standard output:

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You should see something like this:

1184360 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
547664 + 0 mapped (46.24%:-nan%)
1184360 + 0 paired in sequencing
592180 + 0 read1
592180 + 0 read2
473114 + 0 properly paired (39.95%:-nan%)
482360 + 0 with itself and mate mapped
65304 + 0 singletons (5.51%:-nan%)
534 + 0 with mate mapped to a different chr
227 + 0 with mate mapped to a different chr (mapQ>=5)

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The most important statistic is the mapping rate (here 46%) but this readout also allows you to verify that some common expectations (e.g. that about the same number of R1 and R2 reads aligned, and that most mapped reads are proper pairs) are met.

Exercise: What proportion of mapped reads were properly paired?

echo $(( 473114 / 547664 ))
# or
awk 'BEGIN{ print 473114 / 547664 }'

samtools idxstats

Now that we have a sorted, indexed BAM file, we might like to get some simple statistics about the alignment run. For example, we might like to know More information about the alignment is provided by the samtools idxstats report, which shows how many reads aligned to each chromosome/ contig in your reference. The Note that samtools idxstats is a very simple tool that provides this information. If you type the command without any arguments, you will see that it could not be simpler - just type the following command: must be run on a sorted, indexed BAM file.

samtools idxstats yeast_pairedend.sort.bam

The output is a text file with four tab-delimited columns with the following meanings:

1. chromosome name
2. chromosome length
3. number of mapped reads
4. number of unmapped reads

The reason that the "unmapped reads" field for the named chromosomes is not zero is that, if one half of a pair of reads aligns while the other half does not, the unmapped read is still assigned to the chromosome its mate mapped to, but is flagged as unmapped.

Exercise #3: Yeast BWA PE alignment with BioITeam alignment script

Now that you've done everything the hard way, let's see how to do run an alignment pipeline using a BWA alignment script.

First the setup:

mkdir -p $SCRATCH/core_ngs/align2/fastq
cd $SCRATCH/core_ngs/align2/fastq
cp /corral-repl/utexas/BioITeam/core_ngs_tools/alignment/*fastq.gz .

Before executing the script you need to have one environment variable set. We'll do it at the command line here, but you could put it in your .bashrc file.

export path_code=/work/01063/abattenh/code

 | tee yeast_pairedend.idxstats.txt

chrI    230218  8820    1640
chrII   813184  36616   4026
chrIII  316620  13973   1530
chrIV   1531933 72675   8039
chrV    576874  27466   2806
chrVI   270161  10866   1222
chrVII  1090940 50893   5786
chrVIII 562643  24672   3273
chrIX   439888  16246   1739
chrX    745751  31748   3611
chrXI   666816  28017   2776
chrXII  1078177 54783   10124
chrXIII 924431  40921   4556
chrXIV  784333  33070   3703
chrXV   1091291 48714   5150
chrXVI  948066  44916   5032
chrM    85779   3268    291
*       0       0       571392

The output has four tab-delimited columns:

1. contig name
2. contig length
3. number of mapped reads
4. number of unmapped reads

The reason that the "unmapped reads" field for named chromosomes is not zero is that the aligner may initially assign a potential mapping (contig name and start coordinate) to a read, but then mark it later as unampped if it does meet various quality thresholds.

Exercise #3: BWA PE alignment with BioITeam script

Now that you've done everything the hard way, let's see how to do run an alignment pipeline using a BWA alignment script maintained by the BioITeam

First the setup, to work in a new directory:

mkdir -p $SCRATCH/core_ngs/alignment/bwa_script
cd $SCRATCH/core_ngs/alignment/bwa_script
ln -s -f ../../fastq

The BioITeam BWA alignment script is /work/projects/BioITeam/common/script/align_bwa_illumina.sh. Type in the script name to see its usage.

align_bwa_illumina.sh 2017_09_07
Align Illumina SE or PE data with bwa. Produces a sorted, indexed,
duplicate-marked BAM file and various statistics files. Usage:

align_bwa_illumina.sh <aln_mode> <in_file> <out_pfx> <assembly> [ paired trim_sz trim_sz2 seq_fmt qual_fmt ]

Required arguments:
  aln_mode  Alignment mode, either global (bwa aln) or local (bwa mem).
  in_file   For single-end alignments, path to input sequence file.
            For paired-end alignments using fastq, path to the the R1
            fastq file which must contain the string 'R1' in its name.
            The corresponding 'R2' must have the same path except for 'R1'.
  out_pfx   Desired prefix of output files in the current directory.
  assembly  One of hg38, hg19, hg38, mm10, mm9, sacCer3, sacCer1, ce11, ce10,
            danRer7, hs_mirbase, mm_mirbase, or reference index prefix.
Optional arguments:
  paired    0 = single end alignment (default); 1 = paired end.
  trim_sz   Size to trim reads to. Default 0 (no trimming)
  trim_sz2  Size to trim R2 reads to for paired end alignments.
            Defaults to trim_sz
  seq_fmt   Format of sequence file (fastq, bam or scarf). Default is
            fastq if the input file has a '.fastq' extension; scarf
            if it has a '.sequence.txt' extension.
  qual_type Type of read quality scores (sanger, illumina or solexa).
            Default is sanger for fastq, illumina for scarf.
Environment variables:
  show_only  1 = only show what would be done (default not set)
  aln_args   other bowtie2 options (e.g. '-T 20' for mem, '-l 20' for aln)
  no_markdup 1 = don't mark duplicates (default 0, mark duplicates)
  run_fastqc 1 = run fastqc (default 0, don't run). Note that output
             will be in the directory containing the fastq files.
  keep       1 = keep unsorted BAM (default 0, don't keep)
  bwa_bin    BWA binary to use. Default bwa 0.7.x. Note that bwa 0.6.2
             or earlier should be used for scarf and other short reads.
  also: NUM_THREADS, BAM_SORT_MEM, SORT_THREADS, JAVA_MEM_ARG

Examples:
  align_bwa_illumina.sh local  ABC_L001_R1.fastq.gz my_abc hg38 1
  align_bwa_illumina.sh global ABC_L001_R1.fastq.gz my_abc hg38 1 50
  align_bwa_illumina.sh global sequence.txt old sacCer3 0 '' '' scarf solexa

There are lots of bells and whistles in the arguments, but the most important are the first few:

1. aln_mode – whether to perform a global or local alignment (the 1st argument must be one of those words)
   
   • global mode uses the bwa aln workflow as we did above
   • local mode uses the bwa mem command
2. FASTQ file – full or relative path to the FASTQ file (just the R1 fastq if paired end). Can be compressed (.gz)
3. output prefix – prefix for all the output files produced by the script. Should relate back to what the data is.
4. assembly – genome assembly to use.
   • there are pre-built indexes for some common eukaryotes (hg19, hg18, mm10, mm9, danRer7, sacCer3) that you can use
   • or provide a full path for a bwa reference index you have built somewhere
5. paired flag – 0 means single end (the default); 1 means paired end
6. hard trim length – if you want the FASTQ hard trimmed down to a specific length before alignment, supply that number here

We're going to run this script and a similar Bowtie2 alignment script, on the yeast data using the TACC batch system. Copy over the commands file and take a look at it:Now change into the directory and call the script with no arguments to see usage

cd $SCRATCH/core_ngs/alignment/align2
$pathbwa_code/script
cp $CORENGS/align/tacc/aln_script.cmds .
cat aln_script.cmds

align_bwa_illumina.sh

There are lots of bells and whistles in the arguments, but the most important are the first few:

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• there are pre-built indexes for some common eukaryotes (hg19, hg18, mm10, mm9, danRer7, sacCer3) that you can use
• or provide a full path for a bwa reference index you have built somewhere

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 ./fastq/Sample_Yeast_L005_R1.cat.fastq.gz yeast_chip sacCer3 1

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in both global and local alignment modes, and also ru

Now run the pipeline. By piping the output to tee <filename> we can see the script's progress at the terminal, and it also is written to <filename>.

cd $SCRATCH/core_ngs/alignment/bwa_script
$path_code/script/align/align_bwa_illumina.sh ./fastq/Sample_Yeast_L005_R1.cat.fastq.gz yeast_chip sacCer3 1 2>&1 | tee aln.yeast_chip.log

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