fastq.gz how to split.

Question

[Andy]

Good morning everyone,

I am download the fastq files for study GSE132802 through https://www.ebi.ac.uk/ena/browser/view/PRJNA549083. This is paired fastq file, but I only got one fastq file. I am considering split it. But I am not sure what is the best way to do it.

I hope you guys could help me out.

Best Andy

Answer 1

[GenoMax]

PRJNA* is a study identifier. There are a total of 14 samples. You will need to download each sample individually. Sample can be split correctly while it is being downloaded using sra-toolkit.

An example that downloads 1 read for one sample is shown below.

You will get three files per sample. File _1 is Illumina index. FIle _2 is cell barcode+UMI. File _3 is the RNA read.

$ fastq-dump -X 1 -F --split-files SRR9307698

$ head -4 SRR9307698_*
==> SRR9307698_1.fastq <==
@J00177:114:HN7WLBBXX:1:1101:1347:1156
CGCTATGT
+J00177:114:HN7WLBBXX:1:1101:1347:1156
AAA<F7A<

==> SRR9307698_2.fastq <==
@J00177:114:HN7WLBBXX:1:1101:1347:1156
NGATTTCTCTTAACCTACCCTTTAAG
+J00177:114:HN7WLBBXX:1:1101:1347:1156
#-AAFFFJJAFJJJJJJJJJAJJJJA

==> SRR9307698_3.fastq <==
@J00177:114:HN7WLBBXX:1:1101:1347:1156
GNTNCNNGTANCNCTGNCAGAAGGCGGNGNACACNTNGNCNCAGGAANTCCNGANCACGCTCTGGCCCAGGAAANACTTCACCATCGTCCCGGCCGAA
+J00177:114:HN7WLBBXX:1:1101:1347:1156
A#A#<##FAF#J#J<F#JJFJJJFJJ-#F#FJFJ#J#J#J#JJJFJJ#FAJ#JJ#JJFFJFJJAJJJJJJ<7JJ#JJJ<FJJJJJJJJJJJ7JJJAAJ

[Andy]

Thank you!