[Linux] fastq 파일 read 수 확인하기

 

1. 리눅스에서 바로 확인하기

for i in ./*.fastq.gz; do     echo "${i}: $(echo "scale=0; $(zcat "${i}" | wc -l)/4" | bc)" ; done >>counts.txt

 

출력물 ↓

 

./001AcCUSw_trim_1.fastq.gz: 58358
./001AcCUSw_trim_2.fastq.gz: 58358
./001AcLUSw_3_trim_1.fastq.gz: 57066
./001AcLUSw_3_trim_2.fastq.gz: 57066
./001AcLUSw_4_trim_1.fastq.gz: 59239
./001AcLUSw_4_trim_2.fastq.gz: 59239
./001AcRUSw_1_trim_1.fastq.gz: 61334
./001AcRUSw_1_trim_2.fastq.gz: 61334
./001AcRUSw_2_trim_1.fastq.gz: 52160
./001AcRUSw_2_trim_2.fastq.gz: 52160

 

2. Seqkit을 사용하기

conda install -c bioconda seqkit

seqkit stats  *.fastq.gz
# 결과물을 stats.tsv로 저장하고 싶다면 
seqkit stats -To stats.tsv *.fastq.gz

 

출력물↓

 

file    format  type    num_seqs    sum_len min_len avg_len max_len
PHB_Rep1_R1.fastq.gz    FASTQ   RNA 118571  11857100    100 100.0   100
PHB_Rep1_R2.fastq.gz    FASTQ   RNA 118571  11857100    100 100.0   100
PHB_Rep2_R1.fastq.gz    FASTQ   RNA 144826  14482600    100 100.0   100
PHB_Rep2_R2.fastq.gz    FASTQ   RNA 144826  14482600    100 100.0   100
PHB_Rep3_R1.fastq.gz    FASTQ   RNA 129786  12978600    100 100.0   100
PHB_Rep3_R2.fastq.gz    FASTQ   RNA 129786  12978600    100 100.0   100
PUH_Rep1_R1.fastq.gz    FASTQ   RNA 227392  22739200    100 100.0   100
PUH_Rep1_R2.fastq.gz    FASTQ   RNA 227392  22739200    100 100.0   100
PUH_Rep2_R1.fastq.gz    FASTQ   RNA 162373  16237300    100 100.0   100
PUH_Rep2_R2.fastq.gz    FASTQ   RNA 162373  16237300    100 100.0   100
PUH_Rep3_R1.fastq.gz    FASTQ   RNA 185442  18544200    100 100.0   100
PUH_Rep3_R2.fastq.gz    FASTQ   RNA 185442  18544200    100 100.0   100

 

 

 

| 참고

- https://bioinformatics.stackexchange.com/questions/20509/how-to-get-a-file-with-the-number-of-reads-for-several-fastq-gz-files

- https://www.biostars.org/p/139006/