# Bioinformatics

## We can align reads to a genome

There are several tools used to map reads to a genome

• bwa
• bowtie
• bowtie2
• hisat
• hisat2

Each one has several options, that you can read in their manual

## Why we want to do this?

• With RNA messengers we measure gene expression
• With DNA from a new individual, we identify polymorphisms
• They may explain some genetic traits
• For a new species of the same genus, this can be used instead of de novo assembly
• For a genome assembled with De Bruijn graphs, we can find the contigs of each read

## Output format

All these tools produce the same kind of files

Sequence Alignment/Mapping (SAM) files are text files

They are big. Sometimes they are encoded in binary

BAM files are Binary SAM files

Humans and all programs can read text files, only some programs can read binary files

## What is the alignment data?

Many lines like this:

SRR507778.1     0       Mito    20158   60      36M     *       0       0
ANTATAATATTATCCCCACGAGGGCCACACATGTGT
?#?;<BBB?BBGGEGGGGDDE8EEDB:?<=?BB?B7
NM:i:1  MD:Z:1A34       AS:i:34 XS:i:0
SRR507778.2     16      XV      767197  60      36M     *       0       0
ACCCATTTCATAATTAATAAGTGGTATATCAGGANG
<?DGEDBHHHHHHHDHFGFHFGFGHG@@A=@;;7#:
NM:i:1  MD:Z:34C1       AS:i:34 XS:i:0
SRR507778.3     0       II      569438  60      36M     *       0       0
GNAAGAACCCTTATACTAACAGCAGCATAGGAAAGT
NM:i:1  MD:Z:1C34       AS:i:34 XS:i:0

(these are three long lines, written in several lines)

## What is the alignment data?

Each column in Sequence Alignment/Map (SAM) has a different meaning

Column Name Description
1 QNAME Query template/pair NAME
2 FLAG bitwise FLAG
3 RNAME Reference sequence NAME
4 POS 1-based leftmost POSition/coordinate of clipped sequence
5 MAPQ MAPping Quality (Phred-scaled)
6 CIGAR extended CIGAR string
7 MRNM Mate Reference sequence NaMe (= if same as RNAME)
8 MPOS 1-based Mate POSition
9 TLEN inferred Template LENgth (insert size)
10 SEQ query SEQuence on the same strand as the reference
11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE

## What is the flag?

Each bit in the FLAG field is defined as:

Value Code Meaning
1 p the read is paired in sequencing
2 P the read is mapped in a proper pair
4 u the query sequence itself is unmapped
8 U the mate is unmapped
16 r strand of the query (1 for reverse)
32 R strand of the mate
64 1 the read is the first read in a pair
128 2 the read is the second read in a pair
256 s the alignment is not primary
512 f the read fails platform/vendor quality checks
1024 d the read is either a PCR or an optical duplicate
2048 S the alignment is supplementary

## What is a bit flag?

The FLAG column is a number

It is the sum of numbers on the previous table

For example

SRR507778.1     0       ...
SRR507778.2     16      ...

The first read is not paired, and aligned in the Forward strand

The second read is not paired, and aligned in the Reverse strand

## Why there are only 0 and 16 ?

Most of the flags only make sense when we combine forward and reverse read files

bwa mem yeast.fasta y1.fastq y2.fastq > out2.sam

## Now FLAGS is more interesting

99 = 64+32+2+1
• 1 : the read is paired in sequencing
• 2 : the read is mapped in a proper pair
• 32 : strand of the mate
• 64 : the read is the first read in a pair
147 = 128+16+2+1
• 1 : the read is paired in sequencing
• 2 : the read is mapped in a proper pair
• 16 : reverse strand
• 128 : the read is the second read in a pair

## What do we mean by “Paired”?

Each read has its “pair”

fragment      ========================================
PE reads    R1--------->                    <---------R2
unknown gap             ....................
SE
PE

## How to know which reads are paired?

The two FASTQ files need to have the same number of reads

The first read of one file matches the first read of the other file

The n-th read of one file matches the n-th read of the other file

## What do we mean by “proper paired”?

Basically

• Both pairs are in the same chromosome
• both pairs are in opposite strands
• both pairs are facing each other
Good    ---->      <----
bad     ---->      ---->

## Now FLAGS is more interesting

83 = 64+16+2+1
• 1 : the read is paired in sequencing
• 2 : the read is mapped in a proper pair
• 16 : reverse strand
• 64 : the read is the first read in a pair
163 = 128+32+2+1
• 1 : the read is paired in sequencing
• 2 : the read is mapped in a proper pair
• 32 : strand of the mate
• 128 : the read is the second read in a pair

## CIGAR

The column called CIGAR (Concise Idiosyncratic Gapped Alignment Report) describes how the read mapped to the genome

In other words, it shows which operations are necessary to map the read to the reference

For full details see

Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, “The Sequence Alignment/Map format and SAMtools”, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352

## Operations encoded in CIGAR format

 M Alignment (can be a sequence match or mismatch!) I Insertion in the read compared to the reference D Deletion in the read compared to the reference N Skipped region from the reference. An intron (in mRNA) S Soft clipping (clipped sequences are present in read) H Hard clipping (clipped sequences are NOT present in the alignment record); P Padding (silent deletion from padded reference) = Sequence match X Sequence mismatch (not widely used)

## Interpretation

r001 is the name of a read pair. It has FLAG 163 (=1 + 2 + 32 + 128)

• It mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2);
• its mate is mapped to 37 on the reverse strand (32).

Read r002 has three soft-clipped (unaligned) bases

• The coordinate shown in SAM is the position of the first aligned base.
• The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences.

## Interpretation (cont)

The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand.

The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches.

Read r004 is aligned across an intron, indicated by the N operation.

## Another example

What do you see here?

# How to do your own alignments?

## Use Galaxy

If you have a good super-computer, and you know how to use it, then you can do it easily

For small projects it is better to use galaxy

https://usegalaxy.org/