Zcat File Size and Possible Error

[arcolombo698]

Hello.

I have a sample that was ran on two different lanes and was paired end read. so this sample has 4 fastq.gz files.

So I zcat the files on different lane, but the same read.

zcat CHLA-122_S3_L001_R2_001.fastq.gz CHLA-122_S3_L002_R2_001.fastq.gz | gzip > CHLA-122_R2.fastq

Yet when merging the CHLA-122 lanes, Lane1_read1 has size 1854 MiB with lane2_Read1 with size 1853 MiB

but the total size is 3051 ,

I expected the file size to be the sum of the two sizes... roughly
about 3707 MiB, instead I have a difference of 656 MiB


Is this correct zcat command correct???

AC

[dariober]

Hi- I think it's ok to see that the concatenated file has different size from the sum of the inputs. This should be a consequences of the zipping algorithm. (Sometimes paired fastq files have different size even if they contain the same number of characters.)

By the way, if you want to concatenate gzipped files into a single gzip file, you don't need to uncompress and recompress. You can just do

cat file1.gz file2.gz file3.gz > big.gz

Dario