Select reads randomly or split reads into two files

Subsampling single reads (FASTQ):

cat single.fastq | awk '{ printf("%s",$0); n++; if(n%4==0) {
printf("\n");} else { printf("\t");} }' |
awk -v k=10000 'BEGIN{srand(systime() + PROCINFO["pid"]);}{s=x++<k?x1:int(rand()*x);if(s<k)R[s]=$0}END{for(i
in R)print R[i]}' |
awk -F"\t" '{print $1"\n"$2"\n"$3"\n"$4 > "single_sub.fastq"}'

ref : How to do it

• python : https://pythonforbiologists.com/randomly-sampling-reads-from-a-fastq-file/
• unix : http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/subsampling_reads.pdf
• sample files for test : http://molb7621.github.io/workshop/Miscellaneous/data.html

Split single reads into two files (FASTQ):

sample(1)

@cluster_71:UMI_CCAATA
CAGCTTTGCAACCATACTCCCCCCGGAACCC
+
<?B?DEB::9>@?@C=?:=<<<:===@?=83
@cluster_82:UMI_TTTTTG
GCTTATGTTTTATAAAAATAAGTTGCCCCAG
+
75;6>>>>DEC7?6CC>A=9=>@C1<<9>12
@cluster_83:UMI_CCAGTC
CTCCCACAGTTCTGCGCCAGAGCGGAAGAGC
+
=:?*>4>;>66;C:612661<2322141=:-
@cluster_87:UMI_TGACAC
GGTTGAGCACAGGGTACTTTATTGATGGTAC
+
=@E@B=B::;;A=?A=9DEB9ECB8?B@@97

cat test.fq | awk '{ printf("%s", $0); n++; if(n%4==0) { printf("\n");} else { printf("\t");}}' | awk 'NR%2==0' | awk -F"\t" '{print $1"\n"$2"\n"$3"\n"$4 > "even.fq"}'

cat test.fq | awk '{ printf("%s", $0); n++; if(n%4==0) { printf("\n");} else { printf("\t");}}' | awk 'NR%2==1' | awk -F"\t" '{print $1"\n"$2"\n"$3"\n"$4 > "odd.fq"}'

sample(2)

@HWI-ST498:135:H2CKMADXY:2:1101:1183:2117 1:N:0:TGACCA
TGTACACACACACGATGATACATATACATATATATTCCTGATATATATATATATGTGTGTGTCCTGATATATATATATATGTGTGTGTGTGTCAGGAATA
+
4:AAADDF?F8<?C@AEA<<FCCHFFEFBEEBDCGDCGFE<F?@DGIA?B9BBGGBDGB88=F)==FC=@=C@E:D@D4=C?EFE?BBD;;BC36;;;;5
@HWI-ST498:135:H2CKMADXY:2:1101:1210:2118 1:N:0:TGACCA
TCCAGCCTGGGCGAAAGAGTGAAACTCCGTCTCAAAAAATAAAAAGAAAAGAAAAGAAAAGAAAAGAAAATTAGGCCGGTGTGGTGGCACACACCTGTAG
+
4=DDFFFHHHHHJIJJJJJGIJJJJJJJJHIJJJJJJJJJJJJIJJIGIJIHHHHFDFFFEDEEDDDDDDDDDDCDDDDDDDDDABDDDDCDDDBDDDDD
@HWI-ST498:135:H2CKMADXY:2:1101:1176:2176 1:N:0:TGACCA
AAGATGGGAGAGGTTAATTAAGGTGCCGGAGGAAGTGGAAGAGGCCACATTCAGTCCTGAGCAGCCTGACTGCAGGATCCGAAGGCTGGTGTGTTTTGCT
+
@@FFFFFHHHFHJFHIJIJJJJJAFHJJGGIIIJIDGIGGIGHIIJJJJIJGCHGAEHHGFFFFFFEECEADDDDBBDDDDDDBDDDDD<CABBDDDDDD

## tr -d '\r' : remove cr(carriage return)
cat test.fq | awk '{ printf("%s", $0); n++; if(n%4==0) { printf("\n");} else { printf("\t");}}' | tr -d '\r' | awk 'NR%2==1' | awk -F"\t" '{print $1"\n"$2"\n"$3"\n"$4 > "odd.fq"}

ref : Learn about “awk”

• Print odd-numbered lines, print even-numbered lines : https://unix.stackexchange.com/questions/26723/print-odd-numbered-lines-print-even-numbered-lines
• awk if, for statement : http://blog.naver.com/PostView.nhn?blogId=illi0001&logNo=140112045181&redirect=Dlog&widgetTypeCall=true
• awk : http://yacht.yonsei.ac.kr/doku.php?id=yais:linux:manage:awk