Hi members,
I'm facing something weird. I know not all reads in the fastq files can have same length.
But in my trimmed data, read length of reverse and forward files are different. I checked out for only first read, though.
Data: paired end
Organism: E. coli
Output 101 from reverse strand:
Output 54 from forward strand:
An icing to this dilemma is, SPAdes uses 55 as K-mer during assembly. And the genome size from assembly is reasonable.
My questions:
1) Shouldn't SPAdes select K-mer less than 55 here?
I'm facing something weird. I know not all reads in the fastq files can have same length.
But in my trimmed data, read length of reverse and forward files are different. I checked out for only first read, though.
Data: paired end
Organism: E. coli
Output 101 from reverse strand:
Code:
zcat sample_R2_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}' | head -1
Code:
zcat sample_R1_trimmed.fastq.gz | awk '{if(NR%4==2) print length($1)}' | head -1
My questions:
1) Shouldn't SPAdes select K-mer less than 55 here?
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