Mick at 11:48, 20 November 2025

2025-11-20T11:48:31Z

← Older revision		Revision as of 13:48, 20 November 2025
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			<H2>Solutions</H2>

	~~<H2> Solutions </H2>~~		== First look at data ==


	~~Illumina~~ data:
	1.

			1. Navigate to home directory.
	<pre>		<pre>
	cd		cd
	</pre>		</pre>

			2. Create directory <tt>first_look</tt>.
	2.

	<pre>		<pre>
	mkdir first_look/		mkdir first_look
			cd first_look
	</pre>		</pre>

	3.		3. Copy FASTQ file.

	<pre>		<pre>
	cp /~~data~~/~~shared~~/exercises/first_look/reads.fastq.gz .		cp /home/projects/22126_NGS/exercises/first_look/reads.fastq.gz .
	</pre>		</pre>

	4.		4. Inspect reads.

	<pre>		<pre>
	zless -S reads.fastq.gz		zless -S reads.fastq.gz
	</pre>		</pre>

			5. Count number of reads (lines / 4).
	5.

	<pre>		<pre>
	zcat ~~/data/shared/exercises/first_look/~~reads.fastq.gz \|wc -l		zcat reads.fastq.gz \| wc -l
	</pre>		</pre>

	1000 lines		If result = 1000 lines →
			1000 / 4 = <b>250 reads</b>.

	~~so 1000/4 250 sequences.~~		---

	1.		== Illumina data ==

			1. Extract paired-end data.
	<pre>		<pre>
	tar xvfz /~~data~~/~~shared~~/exercises/first_look/pairedReads.tar.gz		tar xvfz /home/projects/22126_NGS/exercises/first_look/pairedReads.tar.gz
	</pre>		</pre>

	2.		This creates:
			* ERR243038_1.fastq
	~~<pre>~~		* ERR243038_2.fastq
	~~head~~ ERR243038_1.fastq ERR243038_2.fastq
	~~</pre>~~

			2. Inspect the first read header in each file.
	<pre>		<pre>
	~~grep @ERR243038~~ ERR243038_1.fastq \|head		head ERR243038_1.fastq
			head ERR243038_2.fastq
	</pre>		</pre>

			Extract first 10 header lines using grep:
	<pre>		<pre>
	grep ~~-m 10~~ @ERR243038 ERR243038_1.fastq		grep '^@ERR243038' ERR243038_1.fastq \| head
			grep '^@ERR243038' ERR243038_2.fastq \| head
	</pre>		</pre>

	~~the~~ output is:		Example output:

	<pre>		<pre>
	@ERR243038.1 HS4_09359:1:1101:1072:21612#33/1		@ERR243038.1 HS4_09359:1:1101:1072:21612#33/1
	@ERR243038.2 HS4_09359:1:1101:1076:69021#33/1		@ERR243038.2 HS4_09359:1:1101:1076:69021#33/1
	@ERR243038.3 HS4_09359:1:1101:1081:60568#33/1		@ERR243038.3 HS4_09359:1:1101:1081:60568#33/1
	~~@ERR243038~~.~~4 HS4_09359:1:1101:1086:81871#33/1~~		...
	~~@ERR243038~~.~~5 HS4_09359:1:1101:1086:82800#33/1~~
	~~@ERR243038~~.~~6 HS4_09359:1:1101:1090:45168#33/1~~
	~~@ERR243038.7 HS4_09359:1:1101:1091:34108#33/1~~
	~~@ERR243038.8 HS4_09359:1:1101:1096:7235#33/1~~
	~~@ERR243038.9 HS4_09359:1:1101:1099:66333#33/1~~
	~~@ERR243038.10 HS4_09359:1:1101:1101:32746#33/1~~
	</pre>		</pre>

			3. Remove trailing /1 and /2 using sed.
			<pre>
			grep '^@ERR243038' ERR243038_1.fastq \| sed 's:/1$::' > human_1.headers
			grep '^@ERR243038' ERR243038_2.fastq \| sed 's:/2$::' > human_2.headers
			</pre>

			(Alternate version using generic regex:
	<pre>		<pre>
	grep @ERR243038 ERR243038_1.fastq \|sed "s/\/1//~~g" \|head~~		grep '^@ERR243038' ERR243038_1.fastq \| sed 's/.$//' > human_1.headers
			grep '^@ERR243038' ERR243038_2.fastq \| sed 's/.$//' > human_2.headers
	</pre>		</pre>
			)

	3.		4. Compare the results.

			View first 10 lines of each:
	<pre>		<pre>
	~~grep @ERR243038 ERR243038_1.fastq \|sed "s/\/1//g" >~~ human_1.headers		head human_1.headers
	~~grep @ERR243038 ERR243038_2.fastq \|sed "s/\/2//g" >~~ human_2.headers		head human_2.headers
	</pre>		</pre>

	4.		Side-by-side:
			<pre>
			paste human_1.headers human_2.headers \| head
			</pre>

			Ensure they match:
	<pre>		<pre>
	~~head human_1.headers~~		diff human_1.headers human_2.headers
	~~head human_2.headers~~
	~~paste human_1.headers human_2.headers~~
	diff human_1.headers human_2.headers
	</pre>		</pre>

			If <code>diff</code> prints nothing, the paired-end files are in perfect sync.

WikiSysop: Created page with "

Solutions

Illumina data: 1.

cd

 mkdir first_look/

 cp /data/shared/exercises/first_look/reads.fastq.gz .

  zless -S reads.fastq.gz

  zcat /data/shared/exercises/first_look/reads.fastq.gz  |wc -l

1000 lines so 1000/4 250 sequences. 1.

 tar xvfz /data/shared/exercises/first_look/pairedReads.tar.gz

 head ERR243038_1.fastq ERR243038_2.fastq

..."

2024-03-19T15:23:15Z

Created page with " <H2> Solutions </H2> Illumina data: 1. <pre> cd </pre> 2. <pre> mkdir first_look/ </pre> 3. <pre> cp /data/shared/exercises/first_look/reads.fastq.gz . </pre> 4. <pre> zless -S reads.fastq.gz </pre> 5. <pre> zcat /data/shared/exercises/first_look/reads.fastq.gz |wc -l </pre> 1000 lines so 1000/4 250 sequences. 1. <pre> tar xvfz /data/shared/exercises/first_look/pairedReads.tar.gz </pre> 2. <pre> head ERR243038_1.fastq ERR243038_2.fastq </pre>..."

New page

<H2> Solutions </H2>

Illumina data:
1.

<pre>
cd
</pre>

2.

<pre>
mkdir first_look/
</pre>

3.

<pre>
cp /data/shared/exercises/first_look/reads.fastq.gz .
</pre>

4.

<pre>
zless -S reads.fastq.gz
</pre>

5.

<pre>
zcat /data/shared/exercises/first_look/reads.fastq.gz |wc -l
</pre>

1000 lines

so 1000/4 250 sequences.

1.

<pre>
tar xvfz /data/shared/exercises/first_look/pairedReads.tar.gz
</pre>

2.

<pre>
head ERR243038_1.fastq ERR243038_2.fastq
</pre>

<pre>
grep @ERR243038 ERR243038_1.fastq |head
</pre>

<pre>
grep -m 10 @ERR243038 ERR243038_1.fastq
</pre>

the output is:

<pre>
@ERR243038.1 HS4_09359:1:1101:1072:21612#33/1
@ERR243038.2 HS4_09359:1:1101:1076:69021#33/1
@ERR243038.3 HS4_09359:1:1101:1081:60568#33/1
@ERR243038.4 HS4_09359:1:1101:1086:81871#33/1
@ERR243038.5 HS4_09359:1:1101:1086:82800#33/1
@ERR243038.6 HS4_09359:1:1101:1090:45168#33/1
@ERR243038.7 HS4_09359:1:1101:1091:34108#33/1
@ERR243038.8 HS4_09359:1:1101:1096:7235#33/1
@ERR243038.9 HS4_09359:1:1101:1099:66333#33/1
@ERR243038.10 HS4_09359:1:1101:1101:32746#33/1
</pre>

<pre>
grep @ERR243038 ERR243038_1.fastq |sed "s/\/1//g" |head
</pre>

3.

<pre>
grep @ERR243038 ERR243038_1.fastq |sed "s/\/1//g" > human_1.headers
grep @ERR243038 ERR243038_2.fastq |sed "s/\/2//g" > human_2.headers
</pre>

4.

<pre>
head human_1.headers
head human_2.headers
paste human_1.headers human_2.headers
diff human_1.headers human_2.headers
</pre>

First look exercise answers - Revision history

Mick at 11:48, 20 November 2025

WikiSysop: Created page with "

Solutions