Why is alignment score dependent on quality score?

Lessen impact of sequencing errors

Which steps for SRR074285?

remove adapter contamination, filter low quality reads

Skip trimming/filtering: effect on mapping?

mapping takes more time, more reads that map to same position, less mapped reads

Why remove very short reads after adapter clipping?

They will complicate the mapping

Where can you obtain the adapter sequence?

FASTQC Overrepresented Sequences

it cannot process compressed files

search for unzip tool in Genepattern

Where can you find the quality encoding?

FASTQC report: Basic statistics module

Why allow mismatches?

sequencing errors, especially at 3'end

FASTQC modules show need to filter low quality reads?

per sequence quality scores, per tile sequence quality

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NGSIntro3

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Questions 16

Answers

1
How many adapters for PE data typically?
0
1
2
more than 2
2
Why is alignment score dependent on quality score?
Simplify the alignment
Lessen impact of sequencing errors
Ignore bases at 3'end of the reads
Mismatches depend on length of reads
3
Which end to trim?
3'
5'
both
4
FASTQC modules show need to filter adapter dimers?
per base sequence quality
per tile sequence quality
overrepresented sequences
basic statistics
5
Which steps for SRR074285?
trim low quality bases from 3'end
remove adapter contamination
filter low quality reads
trim low quality bases from 5'end
6
Skip trimming/filtering: effect on mapping?
mapping takes more time
more reads that map to same position
less mapped reads
less reads that map to many positions
7
Why remove very short reads after adapter clipping?
They are remainders of adapters
All reads must have the same length
They will complicate the mapping
Keep two reads per pair in PE data
8
Where can you obtain the adapter sequence?
Illumina website
FASTQC Overrepresented Sequences
fastq file
Trimmomatic
9
What percentage of reads was discarded?
around 63%
around 31%
no reads discarded
around 14%
10
Why groomer error?
wrong quality encoding
bug in groomer
it cannot process compressed files
error in header of the fastq file
11
How to fix this?
search for the original fastq file online
search for unzip tool in Genepattern
unzip the file on your computer
there's no way to fix this
12
Where can you find the quality encoding?
fastq file
ASCII table
probability file
FASTQC report: Basic statistics module
13
Why is the fastq file not recognized by trimmomatic?
trimmomatic doesn't work in Galaxy
trimmomatic doesn't work on fastq files
file must be in .fastq.gz format
messy file
14
Why allow mismatches?
millions of reads
illumina reads are short
there can be gaps in the alignment
sequencing errors, especially at 3'end
15
FASTQC modules show need to filter low quality reads?
per sequence quality scores
per tile sequence quality
per base sequence quality
per sequence GC content
16
How to solve this?
use a different tool for clipping
gzip the file
use a different version of trimmomatic
groom the file

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