How many unzipped fastq (.fq or .fastq) files are in the directory

How many unzipped fastq (.fq or .fastq) files are in the directory

 

/data/compres/seq_platform_data/

 

 

2. The output of trimming software will also be a fastq file (or multiple fastq files) (True/False)

 

 

3. Which option is specified to run trimmomatic on paired-end sequence data?

PE

-PE

SE

-SE

 

4. What will happen if you execute the command:

fastqc -h

 

fastqc will run default options

fastqc will fail and print an error message because you haven’t specified a fastq file for it to run on

 

fastqc will output the help file and exit

 

 

5. Which of the following can be used to transfer files between a local computer and a high-performance computing cluster?

 

FileZilla

 

sftp

 

Cyberduck

 

ssh

 

mv

6. Which command will enable you to run fastqc on the cluster?

 

module avail fastqc

 

module load fastc

 

module avail fastqc/0.11.7

 

module load fastqc – 0.11.9-gcc-12.1.0

 

 

7. Are the fastq files found in:

 

/data/compres/seq_platform_data/

 

single end or paired end?

8. For the following execution, what is the window size for trimming this single end read

with trimmomatic?

 

interactive

trimmomatic SE illumina.fq illumina.trim.fq SLIDINGWINDOW:4:30

 

 

A. we cannot conclude the window size from this execution

B. there is a randomized window size each time the execution is run

C. 4 base pairs

D. 30 base pairs

E. none of the above answer

 

9. What is the flag you need to use to output the report file from fastqc to a particular

location?

-o

-output

10. You can view the output of fastqc directly in the shell terminal on the cluster. (True/False)

 

 

11. We are working with the fastq files in this directory:

 

/data/compres/seq_platform_data/

 

Generate a fastqc report for each fastq file in that directory.

Look at the “Per base sequence quality” file and compare them, then choose the correct

answers below.

The mean quality of the illumina reads is higher than those of iontorrent, which are both

higher than minion and pacbio

For all fastqc reports, you can see the exact quality of the first 9 bases, then the rest of the

quality scores are binned

You can see the mean quality of every single base across all reads

The binning of base quality scores is the same (e.g., bins have the same number of bases

in them) for all technologies

. You can view the output of fastqc directly in the shell terminal on the cluster. (True/False)

 

 

11. We are working with the fastq files in this directory:

 

/data/compres/seq_platform_data/

 

Generate a fastqc report for each fastq file in that directory.

Look at the “Per base sequence quality” file and compare them, then choose the correct

answers below.

The mean quality of the illumina reads is higher than those of iontorrent, which are both

higher than minion and pacbio

For all fastqc reports, you can see the exact quality of the first 9 bases, then the rest of the

quality scores are binned

You can see the mean quality of every single base across all reads

The binning of base quality scores is the same (e.g., bins have the same number of bases

in them) for all technologies

minion.fq

There are BLANK records/reads/sequences in

pacbio.fq

 

 

The illumina sequence length (or interval) as listed in the fastqc report is:

 

The iontorrent sequence length (or interval) as listed in the fastqc report is:

 

The minion sequence length (or interval) as listed in the fastqc report is:

 

The pacbio sequence length (or interval) as listed in the fastqc report is:

 

 

13. Run trimmomatic on all fastq files in:

/data/compres/seq_platform_data

Use default trimming parameters for these single-end sequencing files, with the options

being a sliding window of 4, with minimum phred quality of 30.

 

SLIDINGWINDOW:4:30

 

HINT: Trimmomatic uses the first few thousand reads to guess the Phred encoding of the

file, looking for unique characters from the Phred+33 or Phred+64 set. If it can’t find,

trimmomatic will give you an error:

 

Error: Unable to detect quality encoding

 

If you are getting an error on any of your runs, you can specify the encoding (Phred+33)

via the command line with the flag:

 

-phred33

 

For each of these files, please report the total surviving reads and total dropped reads

(not the percentages):

Illumina:

Surviving:

Dropped:

 

IonTorrent:

Surviving:

Dropped:

 

PacBio:

Surviving:

Dropped:

 

Minion:

Surviving:

Dropped: