My current command is the following:
reformat.sh in=./ERR1701760.fastq out=stdout.fastq overwrite=t samplereadstarget=10000 sampleseed=0 > x.fq
How can I increase the speed of this program for sampling reads? The reason I'm using
reformat.sh is because sometimes I have interleaved reads and I'll need the `R1.
Are there any parameters I can adjust? I know I can just take the first 10000 reads which will be much faster but I want to be able to use different random seeds here.
109,100,547 (single ended?) reads in
ERR1701760.fastq. I thought originally that these were paired end since these are HISEQ but I feel like I only downloaded the forward reads.
(base) -bash-4.1$ head ERR1701760.fastq @ERR1701760.1 1 length=143 TTACGATTTGCCCAAAAGTCTTTCCCCCGTGTATCATCTCGGAACAGGATACCCACCTTGCCACTGTCGATTACGTCATTATCTTTCATGACGTTGTCGGACTAGCCGAAAAAAACCTAATTAAGAACANTTCAAGTTTCGGC +ERR1701760.1 1 length=143 @@@FFBDDHFHHHEBD@FCHHIFIIGIGGFHEHHGADHHIIEFGHHICGGHHHIIIIIEEHGGHF@@EB(5@BEB?A=?CDDCC;ACCD>CCBB?BBCBB@@FFDEFHFHHDHGIIIJIIIJJIIIJJG#0?FHGIFHGGIGI @ERR1701760.2 2 length=151 AAATATGTGGATCTGTTCGCTGCCAGTGCCATATTTTGTAAGCGTGGGATTGCACAATGTGGTCGTAACGTTGGTACGGTACAACAAGATTGAGCTGTCCGCAAACATGGGAATCTCCAGAATCTCACAAANTATTGTTCTCCATATTATC +ERR1701760.2 2 length=151 CCCFFFFDHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJIIJJIJJIJJJJJJJJJJJJIHHHHFFFEDDDEDDDDDDDDDDDDDDDDDDDDDDDD?CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJ#1@FHIJIIJJJJJJJJIJH @ERR1701760.3 3 length=156 CACCGACATCCACACGTGCATTCCTCCCGAGACGGACACGTGACGGCAGGCAAGGCCGCGGAAAGGGAAGAATGCGTGGGAGGGAAAGGCCGCGGCGAAGGAAGGTCGCCCTGGTTCGTATGTTTCCTTTGGATATAGATCTTCTCCTCCTCCAAC