Data used in this course

For this course, we will use public data sets from GEO data set GSE76647.


  • Go to the GEO page corresponding to entry GSE76647
  • What is the organism the samples come from? Which types of cells? What is the goal of the experiment?
  • What information do you get about the sequencing protocol?
  • Retrieve the SRA codes corresponding to all samplesfrom the SRA RUN Selector)

Data details

  • Data set GSE76647 has 10 Homo sapiens samples from differentiated (5-day differentiation) and undifferentiated primary keratinocytes.
    Some of the samples underwent a knock-down of the FOXC1 gene:
GEO ID SRA ID Sample name Differentiation Condition
GSM2031982 SRR3091420 5p4_25c undiff WT
GSM2031983 SRR3091421 5p4_27c undiff WT
GSM2031984 SRR3091422 5p4_28c diff 5 days WT
GSM2031985 SRR3091423 5p4_29c diff 5 days WT
GSM2031986 SRR3091424 5p4_30c diff 5 days WT
GSM2031987 SRR3091425 5p4_31cfoxc1 undiff WT
GSM2031988 SRR3091426 5p4_32cfoxc1 undiff WT
GSM2031989 SRR3091427 5p4_33cfoxc1 undiff WT
GSM2031990 SRR3091428 5p4_34cfoxc1 diff 5 days WT
GSM2031991 SRR3091429 5p4_35cfoxc1 diff 5 days WT
  • The raw data can be downloaded as follows, using fastq-dump
# Go to the "raw_data" folder
cd ~/rnaseq_course/raw_data

# Download raw data files
for sra in SRR309142{0,1,2,3,4,5,6,7,8,9}
do echo $sra
$RUN fastq-dump --gzip --origfmt --skip-technical --split-files $sra

In case downloading those files is too slow, we have prepared fastq files that correspond to chromosome 6 only. Please download it:

# go to raw data folder
cd ~/rnaseq_course/raw_data

# archive containing the 6 fastq files for chromosome 6 only

# extract archive
tar -xvzf fastq_chr6.tar.gz

# remove .tar.gz file
rm fastq_chr6.tar.gz
  • How many reads are there per sample?
  • What is the read length?

Number of reads:

cd ~/rnaseq_course/raw_data/fastq_chr6

# With grep
zcat SRR3091420_1_chr6.fastq.gz | grep "^@" | wc -l

# With paste
zcat SRR3091420_1_chr6.fastq.gz | paste - - - - | wc -l

# With awk
zcat SRR3091420_1_chr6.fastq.gz | awk 'BEGIN{i=0}{i++;}END{print i/4}'

For all samples:

for fastq in *fastq.gz
do echo $fastq
zcat $fastq | awk 'BEGIN{i=0}{i++;}END{print i/4}'

Count read length:

# Count read length for all rows
zcat SRR3091420_1_chr6.fastq.gz | paste - - - - | awk '{print length($2)}'

# Summarize
zcat SRR3091420_1_chr6.fastq.gz | paste - - - - | awk '{print length($2)}' | sort | uniq -c