First look exercise answers

Solutions

Illumina data: 1.

cd 

2.

mkdir first_look/

3.

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

4.

 zless -S reads.fastq.gz  

5.

 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

2.

head ERR243038_1.fastq ERR243038_2.fastq

grep @ERR243038  ERR243038_1.fastq |head 

grep -m 10  @ERR243038  ERR243038_1.fastq 

the output is:

@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

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

3.

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

4.

head human_1.headers
head human_2.headers
paste human_1.headers human_2.headers 
diff human_1.headers human_2.headers