fqcheck with multi lane fastq file

[Mingxi-HUANG-Sunnia]

hi， I have multi lanes for read1 and read2， how can I deal with this？
is it possible to enter a list of file，like "fqcheck -InFq1 fq1.list -InFq2 fq2.list -OutStat1 1.fqcheck -OutStat2 2.fqcheck".

fq1.list:
SampeA.lane1_1.fq.gz
SampeA.lane2_1.fq.gz
SampeA.lane3_1.fq.gz

fq2.list:
SampeA.lane1_2.fq.gz
SampeA.lane2_2.fq.gz
SampeA.lane3_2.fq.gz

[hewm2008]

Hello! Currently, the tool does not support entering a list of files as you mentioned. So the command “fqcheck -InFq1 fq1.list -InFq2 fq2.list -OutStat1 1.fqcheck -OutStat2 2.fqcheck” won’t work.

There are two alternative solutions:

Solution 1: Concurrent Runs
You can run the fqcheck command concurrently for each lane. For example, for lane 1, you can use the following command:

fqcheck -InFq1 SampeA.lane1_1.fq.gz -InFq2 SampeA.lane1_2.fq.gz -OutStat1 SampeA.lane1_1.fqcheck -OutStat2 SampeA.lane1_2.fqcheck
fqcheck -InFq1 SampeA.lane2_1.fq.gz -InFq2 SampeA.lane2_2.fq.gz -OutStat1 SampeA.lane2_1.fqcheck -OutStat2 SampeA.lane2_2.fqcheck
fqcheck -InFq1 SampeA.lane3_1.fq.gz -InFq2 SampeA.lane3_2.fq.gz -OutStat1 SampeA.lane3_1.fqcheck -OutStat2 SampeA.lane3_2.fqcheck

Do this for each lane in your dataset.

Solution 2: Concatenation
If you want to process all the lanes together, you can concatenate all the read1 files and all the read2 files respectively. For read1 files, you can use the following command:

zcat SampeA.lane*_1.fq.gz | gzip > SampeALL_1.fq.gz
##  Do the same for read2 files:
zcat SampeA.lane*_2.fq.gz | gzip > SampeALL_2.fq.gz
## Then you can run the fqcheck command on the concatenated files:
fqcheck -InFq1 SampeALL_1.fq.gz -InFq2 SampeALL_2.fq.gz -OutStat1 SampeALL_1.fqcheck -OutStat2 SampeALL_2.fqcheck

Choose the solution that best fits your needs.